{
    "a_galaxy_workflow": "true",
    "annotation": "Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5)",
    "creator": [
        {
            "class": "Organization",
            "name": "Galaxy"
        },
        {
            "class": "Organization",
            "name": "VGP",
            "url": "https://vertebrategenomeproject.org"
        }
    ],
    "format-version": "0.1",
    "license": "CC-BY-4.0",
    "release": "0.3.2", 
    "name": "Purge-duplicate-contigs-VGP6",
    "steps": {
        "0": {
            "annotation": "A simple list containing PacBio data in either fasta or fastq formats with trimmed adapters. These are usually generated by contiging workflows and have tag \"trimmed_hifi\" associated with them.\n",
            "content_id": null,
            "errors": null,
            "id": 0,
            "input_connections": {},
            "inputs": [
                {
                    "description": "A simple list containing PacBio data in either fasta or fastq formats with trimmed adapters. These are usually generated by contiging workflows and have tag \"trimmed_hifi\" associated with them.\n",
                    "name": "Pacbio Reads Collection - Trimmed"
                }
            ],
            "label": "Pacbio Reads Collection - Trimmed",
            "name": "Input dataset collection",
            "outputs": [],
            "position": {
                "left": 0,
                "top": 0
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"trimmed_hifi\", \"collection_type\": \"list\"}",
            "tool_version": null,
            "type": "data_collection_input",
            "uuid": "0df002ab-91cf-4767-a348-9ce31f439a01",
            "when": null,
            "workflow_outputs": []
        },
        "1": {
            "annotation": "Primary assembly generated by contiging workflow in fasta format.",
            "content_id": null,
            "errors": null,
            "id": 1,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Primary assembly generated by contiging workflow in fasta format.",
                    "name": "Hifiasm Primary assembly"
                }
            ],
            "label": "Hifiasm Primary assembly",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 21.7890625,
                "top": 101.30078125
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"hifiasm_hic_hap1\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "158c873a-b3bc-4135-95d4-d435a4849786",
            "when": null,
            "workflow_outputs": []
        },
        "2": {
            "annotation": "Alternate assembly generated by contiging workflow in fasta format.",
            "content_id": null,
            "errors": null,
            "id": 2,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Alternate assembly generated by contiging workflow in fasta format.",
                    "name": "Hifiasm Alternate assembly"
                }
            ],
            "label": "Hifiasm Alternate assembly",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 52.028900146484375,
                "top": 200.42266845703125
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"format\": [\"fasta\"], \"tag\": \"hifiasm_hic_hap2\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "681334cb-47f1-49cb-9f86-612e17655419",
            "when": null,
            "workflow_outputs": []
        },
        "3": {
            "annotation": "Meryl database generated by K-mer profiling workflow.\n",
            "content_id": null,
            "errors": null,
            "id": 3,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Meryl database generated by K-mer profiling workflow.\n",
                    "name": "Meryl Database"
                }
            ],
            "label": "Meryl Database",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 101.96484375,
                "top": 297.9609375
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"meryl_db\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "0c3b5f68-3534-4d76-b291-e844707606ec",
            "when": null,
            "workflow_outputs": []
        },
        "4": {
            "annotation": "GenomeScope model parameters generated by K-mer profiling workflow.\n",
            "content_id": null,
            "errors": null,
            "id": 4,
            "input_connections": {},
            "inputs": [
                {
                    "description": "GenomeScope model parameters generated by K-mer profiling workflow.\n",
                    "name": "Genomescope model parameters"
                }
            ],
            "label": "Genomescope model parameters",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 145.4080810546875,
                "top": 390.35603841145866
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"genomescope_params\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "5c8af4f2-5764-49a6-89fa-dd8730b11828",
            "when": null,
            "workflow_outputs": []
        },
        "5": {
            "annotation": "Estimated genome size generated by contiging workflows. ",
            "content_id": null,
            "errors": null,
            "id": 5,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Estimated genome size generated by contiging workflows. ",
                    "name": "Estimated genome size - Parameter File"
                }
            ],
            "label": "Estimated genome size - Parameter File",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 188.4163818359375,
                "top": 507.23516845703125
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"estimated_genome_size\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "9cc9d8e4-a917-4258-a9fc-74de593c42de",
            "when": null,
            "workflow_outputs": []
        },
        "6": {
            "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis.\n",
            "content_id": null,
            "errors": null,
            "id": 6,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Taxonomic lineage for the organism being assembled for Busco analysis.\n",
                    "name": "Lineage"
                }
            ],
            "label": "Lineage",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 216.70703125,
                "top": 631.06640625
            },
            "tool_id": null,
            "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "a489e27a-9a41-41e2-ab57-db2e855b1018",
            "when": null,
            "workflow_outputs": []
        },
        "7": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 7,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "SAK input file"
                }
            ],
            "label": "SAK input file",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 2647.0749499476224,
                "top": 1846.1729865822142
            },
            "tool_id": null,
            "tool_state": "{\"optional\": true, \"tag\": null}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "f53ab5b0-6b4d-43ea-8876-a1e2476fc7c6",
            "when": null,
            "workflow_outputs": []
        },
        "8": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 8,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "Name of primary assembly"
                }
            ],
            "label": "Name of primary assembly",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 4415.97265625,
                "top": 202.03515625
            },
            "tool_id": null,
            "tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "2952f3e6-cc98-4cbe-ac46-32adb482ff3d",
            "when": null,
            "workflow_outputs": []
        },
        "9": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 9,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "Name of alternate assembly"
                }
            ],
            "label": "Name of alternate assembly",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 4420.62890625,
                "top": 321.19140625
            },
            "tool_id": null,
            "tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "fd024c72-fe6c-4cd9-ac28-c8e86eaafc4f",
            "when": null,
            "workflow_outputs": []
        },
        "10": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "errors": null,
            "id": 10,
            "input_connections": {
                "fastq_input|fastq_input1": {
                    "id": 0,
                    "output_name": "output"
                },
                "reference_source|ref_file": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Map with minimap2",
            "outputs": [
                {
                    "name": "alignment_output",
                    "type": "bam"
                }
            ],
            "position": {
                "left": 1118.17578125,
                "top": 45.06640625
            },
            "post_job_actions": {
                "ChangeDatatypeActionalignment_output": {
                    "action_arguments": {
                        "newtype": "paf"
                    },
                    "action_type": "ChangeDatatypeAction",
                    "output_name": "alignment_output"
                },
                "HideDatasetActionalignment_output": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "alignment_output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "be1d967337e4",
                "name": "minimap2",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"asm5\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.26+galaxy0",
            "type": "tool",
            "uuid": "37c8f9b6-ec2e-43f7-9055-5f4f92436903",
            "when": null,
            "workflow_outputs": []
        },
        "11": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 11,
            "input_connections": {
                "function_select|input": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "split_fasta",
                    "type": "fasta"
                }
            ],
            "position": {
                "left": 1414.81640625,
                "top": 1257.89453125
            },
            "post_job_actions": {
                "HideDatasetActionsplit_fasta": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "split_fasta"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"split_fa\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "bc4c132e-b355-4996-aa7e-11423e4253c5",
            "when": null,
            "workflow_outputs": []
        },
        "12": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
            "errors": null,
            "id": 12,
            "input_connections": {
                "input": {
                    "id": 4,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Compute",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "input"
                }
            ],
            "position": {
                "left": 905.01953125,
                "top": 946.48828125
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
            "tool_shed_repository": {
                "changeset_revision": "6595517c2dd8",
                "name": "column_maker",
                "owner": "devteam",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": \"1.5*c3\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"3*c7\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.0",
            "type": "tool",
            "uuid": "104983c1-2416-47ce-a805-9932cc0300a3",
            "when": null,
            "workflow_outputs": []
        },
        "13": {
            "annotation": "",
            "content_id": "param_value_from_file",
            "errors": null,
            "id": 13,
            "input_connections": {
                "input1": {
                    "id": 5,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": "Estimated genome size",
            "name": "Parse parameter value",
            "outputs": [
                {
                    "name": "integer_param",
                    "type": "expression.json"
                }
            ],
            "position": {
                "left": 4162.67578125,
                "top": 1607.08203125
            },
            "post_job_actions": {
                "RenameDatasetActioninteger_param": {
                    "action_arguments": {
                        "newname": "Estimated Genome size"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "integer_param"
                }
            },
            "tool_id": "param_value_from_file",
            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.1.0",
            "type": "tool",
            "uuid": "66e97598-4765-4430-afd3-df587f986c81",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Estimated Genome Size",
                    "output_name": "integer_param",
                    "uuid": "a6d1a01f-ee44-4faa-a8a1-0f20fde412e8"
                }
            ]
        },
        "14": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "errors": null,
            "id": 14,
            "input_connections": {
                "fastq_input|fastq_input1": {
                    "id": 11,
                    "output_name": "split_fasta"
                },
                "reference_source|ref_file": {
                    "id": 11,
                    "output_name": "split_fasta"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Map with minimap2",
            "outputs": [
                {
                    "name": "alignment_output",
                    "type": "bam"
                }
            ],
            "position": {
                "left": 1709.6757657717624,
                "top": 1173.1835801091086
            },
            "post_job_actions": {
                "ChangeDatatypeActionalignment_output": {
                    "action_arguments": {
                        "newtype": "paf"
                    },
                    "action_type": "ChangeDatatypeAction",
                    "output_name": "alignment_output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "be1d967337e4",
                "name": "minimap2",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": \"1\", \"B\": \"19\", \"O\": \"39\", \"O2\": \"81\", \"E\": \"3\", \"E2\": \"1\", \"z\": \"200\", \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"self-homology\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": \"100\", \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": \"40\", \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.26+galaxy0",
            "type": "tool",
            "uuid": "9bceadad-bf25-46f7-8d3f-d9ab18dde578",
            "when": null,
            "workflow_outputs": []
        },
        "15": {
            "annotation": "",
            "content_id": "Cut1",
            "errors": null,
            "id": 15,
            "input_connections": {
                "input": {
                    "id": 12,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Cut",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 1385.28515625,
                "top": 793.75390625
            },
            "post_job_actions": {},
            "tool_id": "Cut1",
            "tool_state": "{\"columnList\": \"c8\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0.2",
            "type": "tool",
            "uuid": "6fc4a474-db85-4503-8879-4698250564ed",
            "when": null,
            "workflow_outputs": []
        },
        "16": {
            "annotation": "",
            "content_id": "Cut1",
            "errors": null,
            "id": 16,
            "input_connections": {
                "input": {
                    "id": 12,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Cut",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 1380.22265625,
                "top": 1043.83203125
            },
            "post_job_actions": {},
            "tool_id": "Cut1",
            "tool_state": "{\"columnList\": \"c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0.2",
            "type": "tool",
            "uuid": "294539f6-ccc6-4bc3-baec-15a668a80899",
            "when": null,
            "workflow_outputs": []
        },
        "17": {
            "annotation": "",
            "content_id": "param_value_from_file",
            "errors": null,
            "id": 17,
            "input_connections": {
                "input1": {
                    "id": 15,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Parse parameter value",
            "outputs": [
                {
                    "name": "integer_param",
                    "type": "expression.json"
                }
            ],
            "position": {
                "left": 1729.67578125,
                "top": 560.94140625
            },
            "post_job_actions": {
                "HideDatasetActioninteger_param": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "integer_param"
                },
                "TagDatasetActioncalcuts_cutoff": {
                    "action_arguments": {
                        "tags": "p1_calcuts_cutoffs"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "calcuts_cutoff"
                },
                "TagDatasetActionhist": {
                    "action_arguments": {
                        "tags": "p1_calcuts_hist"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "hist"
                },
                "TagDatasetActionpbcstat_cov": {
                    "action_arguments": {
                        "tags": "p1_calcuts_basecov"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "pbcstat_cov"
                }
            },
            "tool_id": "param_value_from_file",
            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.1.0",
            "type": "tool",
            "uuid": "f88e694e-edcf-47b2-905d-b9d5be3886eb",
            "when": null,
            "workflow_outputs": []
        },
        "18": {
            "annotation": "",
            "content_id": "param_value_from_file",
            "errors": null,
            "id": 18,
            "input_connections": {
                "input1": {
                    "id": 16,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Parse parameter value",
            "outputs": [
                {
                    "name": "integer_param",
                    "type": "expression.json"
                }
            ],
            "position": {
                "left": 1664.98828125,
                "top": 879.00390625
            },
            "post_job_actions": {
                "HideDatasetActioninteger_param": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "integer_param"
                }
            },
            "tool_id": "param_value_from_file",
            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "0.1.0",
            "type": "tool",
            "uuid": "56cf2739-93df-4d25-baf5-1d1d8ce4aa0f",
            "when": null,
            "workflow_outputs": []
        },
        "19": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 19,
            "input_connections": {
                "function_select|input": {
                    "id": 10,
                    "output_name": "alignment_output"
                },
                "function_select|section_calcuts|transition": {
                    "id": 18,
                    "output_name": "integer_param"
                },
                "function_select|section_calcuts|upper_depth": {
                    "id": 17,
                    "output_name": "integer_param"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "stat_file",
                    "type": "tabular"
                },
                {
                    "name": "pbcstat_cov",
                    "type": "tabular"
                },
                {
                    "name": "pbcstat_wig",
                    "type": "wig"
                },
                {
                    "name": "hist",
                    "type": "png"
                },
                {
                    "name": "calcuts_log",
                    "type": "txt"
                },
                {
                    "name": "calcuts_cutoff",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 2284.2421875,
                "top": 327.12109375
            },
            "post_job_actions": {
                "TagDatasetActioncalcuts_cutoff": {
                    "action_arguments": {
                        "tags": "p1_calcuts_cutoffs, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "calcuts_cutoff"
                },
                "TagDatasetActioncalcuts_log": {
                    "action_arguments": {
                        "tags": "p1_calcuts_log, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "calcuts_log"
                },
                "TagDatasetActionhist": {
                    "action_arguments": {
                        "tags": "p1_calcuts_hist, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "hist"
                },
                "TagDatasetActionpbcstat_cov": {
                    "action_arguments": {
                        "tags": "p1_calcuts_basecov, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "pbcstat_cov"
                },
                "TagDatasetActionpbcstat_wig": {
                    "action_arguments": {
                        "tags": "p1_calcuts_basecov_wig, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "pbcstat_wig"
                },
                "TagDatasetActionstat_file": {
                    "action_arguments": {
                        "tags": "p1_calcuts_depths, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stat_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"pbcstat\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"pbcstat_options\": {\"max_cov\": \"500\", \"min_map_ratio\": \"0.0\", \"min_map_qual\": null, \"flank\": \"0\", \"primary_alignments\": true}, \"section_calcuts\": {\"min_depth\": \"0.1\", \"low_depth\": \"1\", \"transition\": {\"__class__\": \"ConnectedValue\"}, \"upper_depth\": {\"__class__\": \"ConnectedValue\"}, \"ploidy\": \"-d 0\"}, \"section_hist\": {\"ymin\": null, \"ymax\": null, \"xmin\": null, \"xmax\": null, \"title\": \"Read depth histogram plot\"}, \"output_options\": [\"pbcstat_coverage\", \"pbcstat_wig\", \"depth_stats\", \"histogram\", \"calcuts_cutoff\", \"calcuts_log\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "97ce37f6-db2d-483c-abab-813827929e9b",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Cutoffs for primary assembly",
                    "output_name": "calcuts_cutoff",
                    "uuid": "d2c6d9bd-e28f-4ff1-ac7b-f9068e49a582"
                },
                {
                    "label": "Read Coverage and cutoffs calculation on primary assembly : Histogram plot",
                    "output_name": "hist",
                    "uuid": "2e045d9d-99e4-457f-9cee-691616ed6590"
                }
            ]
        },
        "20": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 20,
            "input_connections": {
                "function_select|coverage": {
                    "id": 19,
                    "output_name": "pbcstat_cov"
                },
                "function_select|cutoffs": {
                    "id": 19,
                    "output_name": "calcuts_cutoff"
                },
                "function_select|input": {
                    "id": 14,
                    "output_name": "alignment_output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "purge_dups_log",
                    "type": "txt"
                },
                {
                    "name": "purge_dups_bed",
                    "type": "bed"
                }
            ],
            "position": {
                "left": 2455.08203125,
                "top": 1344.78515625
            },
            "post_job_actions": {
                "TagDatasetActionpurge_dups_bed": {
                    "action_arguments": {
                        "tags": "p1_purgeoverlap_bed"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "purge_dups_bed"
                },
                "TagDatasetActionpurge_dups_log": {
                    "action_arguments": {
                        "tags": "p1_purgeoverlap_log"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "purge_dups_log"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"purge_dups\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"coverage\": {\"__class__\": \"ConnectedValue\"}, \"cutoffs\": {\"__class__\": \"ConnectedValue\"}, \"min_bad\": \"0.8\", \"min_align\": \"70\", \"min_match\": \"200\", \"min_chain\": \"500\", \"max_gap\": \"20000\", \"double_chain\": {\"chaining_rounds\": \"one\", \"__current_case__\": 1}, \"min_chain_score\": \"10000\", \"max_extend\": \"15000\", \"log_file\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "e724b339-6e6b-498c-a62f-33c1bf8d0a9b",
            "when": null,
            "workflow_outputs": []
        },
        "21": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 21,
            "input_connections": {
                "function_select|bed_input": {
                    "id": 20,
                    "output_name": "purge_dups_bed"
                },
                "function_select|fasta_input": {
                    "id": 1,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "get_seqs_hap",
                    "type": "fasta"
                },
                {
                    "name": "get_seqs_purged",
                    "type": "fasta"
                }
            ],
            "position": {
                "left": 2737.47265625,
                "top": 1214.14453125
            },
            "post_job_actions": {
                "RenameDatasetActionget_seqs_purged": {
                    "action_arguments": {
                        "newname": "Purged Primary Assembly"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "get_seqs_purged"
                },
                "TagDatasetActionget_seqs_hap": {
                    "action_arguments": {
                        "tags": "seq_purged_p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "get_seqs_hap"
                },
                "TagDatasetActionget_seqs_purged": {
                    "action_arguments": {
                        "tags": "p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "get_seqs_purged"
                },
                "TagDatasetActionpurge_dups_bed": {
                    "action_arguments": {
                        "tags": "p1_purgeoverlap_bed"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "purge_dups_bed"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"get_seqs\", \"__current_case__\": 5, \"fasta_input\": {\"__class__\": \"ConnectedValue\"}, \"bed_input\": {\"__class__\": \"ConnectedValue\"}, \"advanced_options\": {\"coverage\": false, \"haplotigs\": false, \"length\": \"10000\", \"min_ratio\": \"0.05\", \"end_trim\": true, \"split\": false, \"min_gap\": \"10000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "a25a74ec-9030-4852-88c4-60dc462cd364",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Purged Primary Assembly",
                    "output_name": "get_seqs_purged",
                    "uuid": "cba2e095-7c28-488c-ba6a-8fb2b1612bc1"
                }
            ]
        },
        "22": {
            "annotation": "",
            "content_id": "cat1",
            "errors": null,
            "id": 22,
            "input_connections": {
                "input1": {
                    "id": 21,
                    "output_name": "get_seqs_hap"
                },
                "queries_0|input2": {
                    "id": 2,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Concatenate datasets",
            "outputs": [
                {
                    "name": "out_file1",
                    "type": "input"
                }
            ],
            "position": {
                "left": 2955.67578125,
                "top": 1020.36328125
            },
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "out_file1"
                },
                "RemoveTagDatasetActionout_file1": {
                    "action_arguments": {
                        "tags": "#p1"
                    },
                    "action_type": "RemoveTagDatasetAction",
                    "output_name": "out_file1"
                }
            },
            "tool_id": "cat1",
            "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"input2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.0.0",
            "type": "tool",
            "uuid": "b81b1694-8694-4b23-8cfe-ec2c92b36808",
            "when": null,
            "workflow_outputs": []
        },
        "23": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
            "errors": null,
            "id": 23,
            "input_connections": {
                "input": {
                    "id": 21,
                    "output_name": "get_seqs_purged"
                },
                "lineage|lineage_dataset": {
                    "id": 6,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Busco",
            "outputs": [
                {
                    "name": "busco_sum",
                    "type": "txt"
                },
                {
                    "name": "busco_table",
                    "type": "tabular"
                },
                {
                    "name": "busco_missing",
                    "type": "tabular"
                },
                {
                    "name": "summary_image",
                    "type": "png"
                }
            ],
            "position": {
                "left": 3285.7071094555,
                "top": 1520.5883525119295
            },
            "post_job_actions": {
                "TagDatasetActionbusco_missing": {
                    "action_arguments": {
                        "tags": "busco_p1_missing, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "busco_missing"
                },
                "TagDatasetActionbusco_sum": {
                    "action_arguments": {
                        "tags": "busco_p1_summ, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "busco_sum"
                },
                "TagDatasetActionbusco_table": {
                    "action_arguments": {
                        "tags": "busco_p1_full, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "busco_table"
                },
                "TagDatasetActionsummary_image": {
                    "action_arguments": {
                        "tags": "busco_p1_img, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "summary_image"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "2a5b8b9936bf",
                "name": "busco",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"adv\": {\"evalue\": \"0.001\", \"limit\": \"3\", \"contig_break\": \"10\"}, \"busco_mode\": {\"mode\": \"geno\", \"__current_case__\": 0, \"miniprot\": false, \"use_augustus\": {\"use_augustus_selector\": \"no\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"lineage\": {\"lineage_mode\": \"select_lineage\", \"__current_case__\": 1, \"lineage_dataset\": {\"__class__\": \"ConnectedValue\"}}, \"lineage_conditional\": {\"selector\": \"download\", \"__current_case__\": 1}, \"outputs\": [\"short_summary\", \"missing\", \"image\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "5.5.0+galaxy0",
            "type": "tool",
            "uuid": "88073363-2f5c-4486-a23a-1cfdc4f5e6a6",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Busco on Purged Primary assembly: short summary",
                    "output_name": "busco_sum",
                    "uuid": "87515aeb-4e2e-494f-a271-44013d0944e4"
                },
                {
                    "label": "Busco on Purged Primary assembly: summary image",
                    "output_name": "summary_image",
                    "uuid": "d1ecf9fe-3f76-465d-bcac-cf5b4986a8e8"
                }
            ]
        },
        "24": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "errors": null,
            "id": 24,
            "input_connections": {
                "input_file": {
                    "id": 21,
                    "output_name": "get_seqs_purged"
                },
                "mode_condition|swiss_army_knife": {
                    "id": 7,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats",
            "outputs": [
                {
                    "name": "output",
                    "type": "fastq"
                }
            ],
            "position": {
                "left": 3638.4140625,
                "top": 1864.09765625
            },
            "post_job_actions": {
                "TagDatasetActionoutput": {
                    "action_arguments": {
                        "tags": "p1_gfa,PurgedPrimaryAssembly"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "3ef480892a9f",
                "name": "gfastats",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"500\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3.6+galaxy0",
            "type": "tool",
            "uuid": "55a89d15-73d3-4e8b-b9da-06e650bd00cf",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Purged Primary Assembly (gfa)",
                    "output_name": "output",
                    "uuid": "e04e7950-3bcf-46e8-918c-781f71ef64c9"
                }
            ]
        },
        "25": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "errors": null,
            "id": 25,
            "input_connections": {
                "input_file": {
                    "id": 21,
                    "output_name": "get_seqs_purged"
                },
                "mode_condition|statistics_condition|expected_genomesize": {
                    "id": 13,
                    "output_name": "integer_param"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats",
            "outputs": [
                {
                    "name": "stats",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 4895.80078125,
                "top": 888.28515625
            },
            "post_job_actions": {
                "TagDatasetActionstats": {
                    "action_arguments": {
                        "tags": "gfastats_p1, #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stats"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "3ef480892a9f",
                "name": "gfastats",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3.6+galaxy0",
            "type": "tool",
            "uuid": "68dd6694-1839-4ec3-b258-c30a35901ebf",
            "when": null,
            "workflow_outputs": []
        },
        "26": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "errors": null,
            "id": 26,
            "input_connections": {
                "input_file": {
                    "id": 21,
                    "output_name": "get_seqs_purged"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats",
            "outputs": [
                {
                    "name": "stats",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 4895.86328125,
                "top": 1122.89453125
            },
            "post_job_actions": {
                "TagDatasetActionstats": {
                    "action_arguments": {
                        "tags": "gfastats_contigs_p1,  #p1"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stats"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "3ef480892a9f",
                "name": "gfastats",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3.6+galaxy0",
            "type": "tool",
            "uuid": "2a8b5983-7a56-420d-9825-5ba18ac1e560",
            "when": null,
            "workflow_outputs": []
        },
        "27": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "errors": null,
            "id": 27,
            "input_connections": {
                "fastq_input|fastq_input1": {
                    "id": 0,
                    "output_name": "output"
                },
                "reference_source|ref_file": {
                    "id": 22,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Map with minimap2",
            "outputs": [
                {
                    "name": "alignment_output",
                    "type": "bam"
                }
            ],
            "position": {
                "left": 3254.25390625,
                "top": 655.11328125
            },
            "post_job_actions": {
                "ChangeDatatypeActionalignment_output": {
                    "action_arguments": {
                        "newtype": "paf"
                    },
                    "action_type": "ChangeDatatypeAction",
                    "output_name": "alignment_output"
                },
                "TagDatasetActionalignment_output": {
                    "action_arguments": {
                        "tags": "readCoverage"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "alignment_output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "be1d967337e4",
                "name": "minimap2",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": null, \"B\": null, \"O\": null, \"O2\": null, \"E\": null, \"E2\": null, \"z\": null, \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"asm5\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": null, \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": null, \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.26+galaxy0",
            "type": "tool",
            "uuid": "895ca00e-3eaf-4c8a-9147-be1d62459cf9",
            "when": null,
            "workflow_outputs": []
        },
        "28": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 28,
            "input_connections": {
                "function_select|input": {
                    "id": 22,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "split_fasta",
                    "type": "fasta"
                }
            ],
            "position": {
                "left": 3275.16015625,
                "top": 919.81640625
            },
            "post_job_actions": {
                "HideDatasetActionsplit_fasta": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "split_fasta"
                },
                "RemoveTagDatasetActionsplit_fasta": {
                    "action_arguments": {
                        "tags": "#p1"
                    },
                    "action_type": "RemoveTagDatasetAction",
                    "output_name": "split_fasta"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"split_fa\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "f14c9eb4-89f8-4697-9267-ea58035a9126",
            "when": null,
            "workflow_outputs": []
        },
        "29": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
            "errors": null,
            "id": 29,
            "input_connections": {
                "infile": {
                    "id": 25,
                    "output_name": "stats"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Text reformatting",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 5238.44140625,
                "top": 1132.58203125
            },
            "post_job_actions": {
                "HideDatasetActionoutfile": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
            "tool_shed_repository": {
                "changeset_revision": "d698c222f354",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"code\": \"BEGIN{print \\\"Metric\\\\tPrimary\\\"}; {print}; \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.1.2",
            "type": "tool",
            "uuid": "8ad0b9e5-e002-402d-9d3a-ec20c331f864",
            "when": null,
            "workflow_outputs": []
        },
        "30": {
            "annotation": "",
            "id": 30,
            "input_connections": {
                "gfa_stats": {
                    "id": 26,
                    "input_subworkflow_step_id": 0,
                    "output_name": "stats"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats_data_prep",
            "outputs": [],
            "position": {
                "left": 5764.59765625,
                "top": 329.87890625
            },
            "subworkflow": {
                "a_galaxy_workflow": "true",
                "annotation": "",
                "format-version": "0.1",
                "name": "gfastats_data_prep",
                "steps": {
                    "0": {
                        "annotation": "",
                        "content_id": null,
                        "errors": null,
                        "id": 0,
                        "input_connections": {},
                        "inputs": [
                            {
                                "description": "",
                                "name": "gfa_stats"
                            }
                        ],
                        "label": "gfa_stats",
                        "name": "Input dataset",
                        "outputs": [],
                        "position": {
                            "left": 0.0,
                            "top": 189.90056800842285
                        },
                        "tool_id": null,
                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                        "tool_version": null,
                        "type": "data_input",
                        "uuid": "6f1d6192-d1ef-4117-b3af-436b08bffb72",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "1": {
                        "annotation": "",
                        "content_id": "sort1",
                        "errors": null,
                        "id": 1,
                        "input_connections": {
                            "input": {
                                "id": 0,
                                "output_name": "output"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Sort",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 302.6136245727539,
                            "top": 0.0
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "sort1",
                        "tool_state": "{\"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.2.0",
                        "type": "tool",
                        "uuid": "3000707c-422b-4e57-b965-b06a7b9d824a",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "2": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                        "errors": null,
                        "id": 2,
                        "input_connections": {
                            "infile": {
                                "id": 1,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Text reformatting",
                        "outputs": [
                            {
                                "name": "outfile",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 292.1306838989258,
                            "top": 235.1562442779541
                        },
                        "post_job_actions": {
                            "HideDatasetActionoutfile": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "outfile"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                        "tool_shed_repository": {
                            "changeset_revision": "d698c222f354",
                            "name": "text_processing",
                            "owner": "bgruening",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"code\": \"{total += $2; $3 = total}1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.1.2",
                        "type": "tool",
                        "uuid": "eb19b23a-04eb-4cf6-8389-ca7c21458194",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "3": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
                        "errors": null,
                        "id": 3,
                        "input_connections": {
                            "in_file": {
                                "id": 2,
                                "output_name": "outfile"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Datamash",
                        "outputs": [
                            {
                                "name": "out_file",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 595.0994338989258,
                            "top": 116.0227222442627
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
                        "tool_shed_repository": {
                            "changeset_revision": "4c07ddedc198",
                            "name": "datamash_ops",
                            "owner": "iuc",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"grouping\": \"\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"absmax\", \"op_column\": \"3\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.8+galaxy0",
                        "type": "tool",
                        "uuid": "4beb22a7-74f7-4dff-abf9-3d1bfd263ecd",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "4": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "errors": null,
                        "id": 4,
                        "input_connections": {
                            "input": {
                                "id": 2,
                                "output_name": "outfile"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Add column",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 479.0482864379883,
                            "top": 456.17896461486816
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "tool_shed_repository": {
                            "changeset_revision": "023f0a3760b3",
                            "name": "add_value",
                            "owner": "devteam",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.0.1",
                        "type": "tool",
                        "uuid": "fdf47dde-b43d-431e-a8a4-7f476ada62ae",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "5": {
                        "annotation": "",
                        "content_id": "param_value_from_file",
                        "errors": null,
                        "id": 5,
                        "input_connections": {
                            "input1": {
                                "id": 3,
                                "output_name": "out_file"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Parse parameter value",
                        "outputs": [
                            {
                                "name": "integer_param",
                                "type": "expression.json"
                            }
                        ],
                        "position": {
                            "left": 693.4658889770508,
                            "top": 299.4318027496338
                        },
                        "post_job_actions": {
                            "HideDatasetActioninteger_param": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "integer_param"
                            }
                        },
                        "tool_id": "param_value_from_file",
                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "0.1.0",
                        "type": "tool",
                        "uuid": "f7687678-170e-4287-973d-ee285e5a4d62",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "6": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
                        "errors": null,
                        "id": 6,
                        "input_connections": {
                            "components_1|param_type|component_value": {
                                "id": 5,
                                "output_name": "integer_param"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Compose text parameter value",
                        "outputs": [
                            {
                                "name": "out1",
                                "type": "expression.json"
                            }
                        ],
                        "position": {
                            "left": 885.0994338989258,
                            "top": 493.36646461486816
                        },
                        "post_job_actions": {
                            "HideDatasetActionout1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
                        "tool_shed_repository": {
                            "changeset_revision": "e188c9826e0f",
                            "name": "compose_text_param",
                            "owner": "iuc",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"c3/\"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "0.1.1",
                        "type": "tool",
                        "uuid": "9e083ec1-ee5c-4aa0-83e8-2d4f01db18ca",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "7": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
                        "errors": null,
                        "id": 7,
                        "input_connections": {
                            "input": {
                                "id": 4,
                                "output_name": "out_file1"
                            },
                            "ops|expressions_0|cond": {
                                "id": 6,
                                "output_name": "out1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Compute",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 1115.0993728637695,
                            "top": 735.5255222320557
                        },
                        "post_job_actions": {
                            "RenameDatasetActionout_file1": {
                                "action_arguments": {
                                    "newname": "gfastats data for plotting"
                                },
                                "action_type": "RenameDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
                        "tool_shed_repository": {
                            "changeset_revision": "6595517c2dd8",
                            "name": "column_maker",
                            "owner": "devteam",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "2.0",
                        "type": "tool",
                        "uuid": "9cab2e16-083c-48ed-ada3-566c9639e819",
                        "when": null,
                        "workflow_outputs": [
                            {
                                "label": "gfastats data for plotting",
                                "output_name": "out_file1",
                                "uuid": "5156457e-0da2-4478-a298-7b4612d7e311"
                            }
                        ]
                    }
                },
                "tags": "",
                "uuid": "013a3b3b-83b2-4d3e-928f-998f7176c8a6"
            },
            "tool_id": null,
            "type": "subworkflow",
            "uuid": "509bf106-157c-4565-b2fc-bf28b3818a10",
            "when": null,
            "workflow_outputs": []
        },
        "31": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 31,
            "input_connections": {
                "function_select|input": {
                    "id": 27,
                    "output_name": "alignment_output"
                },
                "function_select|section_calcuts|transition": {
                    "id": 18,
                    "output_name": "integer_param"
                },
                "function_select|section_calcuts|upper_depth": {
                    "id": 17,
                    "output_name": "integer_param"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "stat_file",
                    "type": "tabular"
                },
                {
                    "name": "pbcstat_cov",
                    "type": "tabular"
                },
                {
                    "name": "pbcstat_wig",
                    "type": "wig"
                },
                {
                    "name": "hist",
                    "type": "png"
                },
                {
                    "name": "calcuts_log",
                    "type": "txt"
                },
                {
                    "name": "calcuts_cutoff",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 3614.9135005370044,
                "top": 361.1132969887206
            },
            "post_job_actions": {
                "TagDatasetActioncalcuts_cutoff": {
                    "action_arguments": {
                        "tags": "p2_calcuts_cutoffs"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "calcuts_cutoff"
                },
                "TagDatasetActioncalcuts_log": {
                    "action_arguments": {
                        "tags": " p2_calcuts_log"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "calcuts_log"
                },
                "TagDatasetActionhist": {
                    "action_arguments": {
                        "tags": "p2_calcuts_hist"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "hist"
                },
                "TagDatasetActionpbcstat_cov": {
                    "action_arguments": {
                        "tags": "p2_calcuts_basecov"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "pbcstat_cov"
                },
                "TagDatasetActionpbcstat_wig": {
                    "action_arguments": {
                        "tags": " p2_calcuts_basecov_wig"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "pbcstat_wig"
                },
                "TagDatasetActionpurge_dups_bed": {
                    "action_arguments": {
                        "tags": "p2_purgeoverlap_bed"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "purge_dups_bed"
                },
                "TagDatasetActionstat_file": {
                    "action_arguments": {
                        "tags": "p2_calcuts_depths"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stat_file"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"pbcstat\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}, \"pbcstat_options\": {\"max_cov\": \"500\", \"min_map_ratio\": \"0.0\", \"min_map_qual\": null, \"flank\": \"0\", \"primary_alignments\": true}, \"section_calcuts\": {\"min_depth\": \"0.1\", \"low_depth\": \"1\", \"transition\": {\"__class__\": \"ConnectedValue\"}, \"upper_depth\": {\"__class__\": \"ConnectedValue\"}, \"ploidy\": \"-d 0\"}, \"section_hist\": {\"ymin\": null, \"ymax\": null, \"xmin\": null, \"xmax\": null, \"title\": \"Read depth histogram plot\"}, \"output_options\": [\"pbcstat_coverage\", \"pbcstat_wig\", \"depth_stats\", \"histogram\", \"calcuts_cutoff\", \"calcuts_log\"]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "0496de4b-ec62-48d5-8c36-e2f946ca728d",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Read Coverage and cutoffs calculation on alternate assembly : Histogram Plot",
                    "output_name": "hist",
                    "uuid": "f12c1cc7-a12a-4314-ae16-2738b80afe70"
                },
                {
                    "label": "Cutoffs for alternate assembly",
                    "output_name": "calcuts_cutoff",
                    "uuid": "49bf0c95-0290-4f8b-a9d7-2f17f53e9d26"
                }
            ]
        },
        "32": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "errors": null,
            "id": 32,
            "input_connections": {
                "fastq_input|fastq_input1": {
                    "id": 28,
                    "output_name": "split_fasta"
                },
                "reference_source|ref_file": {
                    "id": 28,
                    "output_name": "split_fasta"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Map with minimap2",
            "outputs": [
                {
                    "name": "alignment_output",
                    "type": "bam"
                }
            ],
            "position": {
                "left": 3648.0662896482727,
                "top": 1119.8737079721939
            },
            "post_job_actions": {
                "ChangeDatatypeActionalignment_output": {
                    "action_arguments": {
                        "newtype": "paf"
                    },
                    "action_type": "ChangeDatatypeAction",
                    "output_name": "alignment_output"
                },
                "TagDatasetActionalignment_output": {
                    "action_arguments": {
                        "tags": "SelfvsSelf"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "alignment_output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.26+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "be1d967337e4",
                "name": "minimap2",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"alignment_options\": {\"splicing\": {\"splice_mode\": \"preset\", \"__current_case__\": 0}, \"A\": \"1\", \"B\": \"19\", \"O\": \"39\", \"O2\": \"81\", \"E\": \"3\", \"E2\": \"1\", \"z\": \"200\", \"z2\": null, \"s\": null, \"no_end_flt\": true}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 0, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"analysis_type_selector\": \"self-homology\"}, \"indexing_options\": {\"H\": false, \"k\": null, \"w\": null, \"I\": null}, \"io_options\": {\"output_format\": \"paf\", \"Q\": false, \"L\": false, \"K\": null, \"cs\": null, \"c\": false, \"eqx\": false, \"Y\": false}, \"mapping_options\": {\"N\": null, \"F\": null, \"f\": null, \"kmer_ocurrence_interval\": {\"interval\": \"\", \"__current_case__\": 1}, \"min_occ_floor\": \"100\", \"q_occ_frac\": \"0.01\", \"g\": null, \"r\": null, \"n\": null, \"m\": \"40\", \"max_chain_skip\": null, \"max_chain_iter\": null, \"X\": false, \"p\": null, \"mask_len\": null}, \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "2.26+galaxy0",
            "type": "tool",
            "uuid": "735ef0da-2e48-404e-b57d-837dc2f161fd",
            "when": null,
            "workflow_outputs": []
        },
        "33": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 33,
            "input_connections": {
                "function_select|coverage": {
                    "id": 31,
                    "output_name": "pbcstat_cov"
                },
                "function_select|cutoffs": {
                    "id": 31,
                    "output_name": "calcuts_cutoff"
                },
                "function_select|input": {
                    "id": 32,
                    "output_name": "alignment_output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "purge_dups_log",
                    "type": "txt"
                },
                {
                    "name": "purge_dups_bed",
                    "type": "bed"
                }
            ],
            "position": {
                "left": 3926.34765625,
                "top": 743.31640625
            },
            "post_job_actions": {
                "TagDatasetActionpurge_dups_bed": {
                    "action_arguments": {
                        "tags": "p2_purgeoverlap_bed"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "purge_dups_bed"
                },
                "TagDatasetActionpurge_dups_log": {
                    "action_arguments": {
                        "tags": "p2_purgeoverlap_log"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "purge_dups_log"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"purge_dups\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}, \"coverage\": {\"__class__\": \"ConnectedValue\"}, \"cutoffs\": {\"__class__\": \"ConnectedValue\"}, \"min_bad\": \"0.8\", \"min_align\": \"70\", \"min_match\": \"200\", \"min_chain\": \"500\", \"max_gap\": \"20000\", \"double_chain\": {\"chaining_rounds\": \"one\", \"__current_case__\": 1}, \"min_chain_score\": \"10000\", \"max_extend\": \"15000\", \"log_file\": true}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "065dcba7-a905-4fc2-8cec-0da64f2cae80",
            "when": null,
            "workflow_outputs": []
        },
        "34": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "errors": null,
            "id": 34,
            "input_connections": {
                "function_select|bed_input": {
                    "id": 33,
                    "output_name": "purge_dups_bed"
                },
                "function_select|fasta_input": {
                    "id": 22,
                    "output_name": "out_file1"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Purge overlaps",
            "outputs": [
                {
                    "name": "get_seqs_hap",
                    "type": "fasta"
                },
                {
                    "name": "get_seqs_purged",
                    "type": "fasta"
                }
            ],
            "position": {
                "left": 4191.601976906268,
                "top": 960.190063897382
            },
            "post_job_actions": {
                "RenameDatasetActionget_seqs_purged": {
                    "action_arguments": {
                        "newname": "Purged Alternate assembly"
                    },
                    "action_type": "RenameDatasetAction",
                    "output_name": "get_seqs_purged"
                },
                "TagDatasetActionget_seqs_hap": {
                    "action_arguments": {
                        "tags": "seq_purged_p2"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "get_seqs_hap"
                },
                "TagDatasetActionget_seqs_purged": {
                    "action_arguments": {
                        "tags": "p2"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "get_seqs_purged"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "e9bd16ba5ebd",
                "name": "purge_dups",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"function_select\": {\"functions\": \"get_seqs\", \"__current_case__\": 5, \"fasta_input\": {\"__class__\": \"ConnectedValue\"}, \"bed_input\": {\"__class__\": \"ConnectedValue\"}, \"advanced_options\": {\"coverage\": false, \"haplotigs\": false, \"length\": \"10000\", \"min_ratio\": \"0.05\", \"end_trim\": true, \"split\": false, \"min_gap\": \"10000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.2.6+galaxy0",
            "type": "tool",
            "uuid": "d38860b9-4bad-4498-b76f-7c5da1d91de0",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Purged Alternate assembly",
                    "output_name": "get_seqs_purged",
                    "uuid": "fc24cb81-cb83-4d9e-8e22-d2e967409f1e"
                }
            ]
        },
        "35": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "errors": null,
            "id": 35,
            "input_connections": {
                "input_file": {
                    "id": 34,
                    "output_name": "get_seqs_purged"
                },
                "mode_condition|statistics_condition|expected_genomesize": {
                    "id": 13,
                    "output_name": "integer_param"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats",
            "outputs": [
                {
                    "name": "stats",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 4886.50390625,
                "top": 450.41015625
            },
            "post_job_actions": {
                "TagDatasetActionstats": {
                    "action_arguments": {
                        "tags": "gfastats_p2, #p2"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stats"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "3ef480892a9f",
                "name": "gfastats",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"assembly\", \"__current_case__\": 2, \"expected_genomesize\": {\"__class__\": \"ConnectedValue\"}}, \"locale\": true, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3.6+galaxy0",
            "type": "tool",
            "uuid": "6ddef707-fe4d-4020-bebb-2ab9b262df62",
            "when": null,
            "workflow_outputs": []
        },
        "36": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "errors": null,
            "id": 36,
            "input_connections": {
                "input_file": {
                    "id": 34,
                    "output_name": "get_seqs_purged"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats",
            "outputs": [
                {
                    "name": "stats",
                    "type": "tabular"
                }
            ],
            "position": {
                "left": 4894.92578125,
                "top": 679.81640625
            },
            "post_job_actions": {
                "TagDatasetActionstats": {
                    "action_arguments": {
                        "tags": "gfastats_contigs_p2, #p2"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stats"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "3ef480892a9f",
                "name": "gfastats",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"statistics\", \"__current_case__\": 1, \"statistics_condition\": {\"selector\": \"size\", \"__current_case__\": 0, \"out_size\": \"c\"}, \"locale\": false, \"tabular\": true, \"discover_paths\": false}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3.6+galaxy0",
            "type": "tool",
            "uuid": "d6ed7c62-c214-4856-a926-2985b003dbd9",
            "when": null,
            "workflow_outputs": []
        },
        "37": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3",
            "errors": null,
            "id": 37,
            "input_connections": {
                "mode|assembly_options|assembly_01": {
                    "id": 21,
                    "output_name": "get_seqs_purged"
                },
                "mode|assembly_options|assembly_02": {
                    "id": 34,
                    "output_name": "get_seqs_purged"
                },
                "mode|meryldb_F1": {
                    "id": 3,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Merqury",
            "outputs": [
                {
                    "name": "qv_files",
                    "type": "input"
                },
                {
                    "name": "png_files",
                    "type": "input"
                },
                {
                    "name": "stats_files",
                    "type": "input"
                },
                {
                    "name": "log_file",
                    "type": "txt"
                }
            ],
            "position": {
                "left": 4745.81640625,
                "top": 1420.23828125
            },
            "post_job_actions": {
                "HideDatasetActionlog_file": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "log_file"
                },
                "TagDatasetActionbed_files": {
                    "action_arguments": {
                        "tags": "merqury_p_bed, #p"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "bed_files"
                },
                "TagDatasetActionpng_files": {
                    "action_arguments": {
                        "tags": "merqury_p_png, #p"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "png_files"
                },
                "TagDatasetActionqv_files": {
                    "action_arguments": {
                        "tags": "merqury_p_qv, #p"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "qv_files"
                },
                "TagDatasetActionsizes_files": {
                    "action_arguments": {
                        "tags": "merqury_p_sizes, #p"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "sizes_files"
                },
                "TagDatasetActionstats_files": {
                    "action_arguments": {
                        "tags": "merqury_p_stats, #p"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "stats_files"
                },
                "TagDatasetActionwig_files": {
                    "action_arguments": {
                        "tags": "merqury_p_wig, #p"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "wig_files"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy3",
            "tool_shed_repository": {
                "changeset_revision": "09c589057ee8",
                "name": "merqury",
                "owner": "iuc",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"label\": \"output_merqury\", \"mode\": {\"options\": \"default\", \"__current_case__\": 0, \"meryldb_F1\": {\"__class__\": \"ConnectedValue\"}, \"assembly_options\": {\"number_assemblies\": \"two\", \"__current_case__\": 1, \"assembly_01\": {\"__class__\": \"ConnectedValue\"}, \"assembly_02\": {\"__class__\": \"ConnectedValue\"}}}, \"output_add_headers\": false, \"output_selector\": [\"qv\", \"plots\", \"stats\", \"log\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3+galaxy3",
            "type": "tool",
            "uuid": "133c60bc-4171-44b4-bf22-c70c623265b2",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Merqury on Phased assemblies: stats",
                    "output_name": "stats_files",
                    "uuid": "70f44477-6a3b-4ac4-b01a-f812ea880bae"
                },
                {
                    "label": "Merqury on Phased assemblies: Images",
                    "output_name": "png_files",
                    "uuid": "ff9cfc96-449e-41d8-9c10-7f586ab6f479"
                }
            ]
        },
        "38": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "errors": null,
            "id": 38,
            "input_connections": {
                "input_file": {
                    "id": 34,
                    "output_name": "get_seqs_purged"
                },
                "mode_condition|swiss_army_knife": {
                    "id": 7,
                    "output_name": "output"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats",
            "outputs": [
                {
                    "name": "output",
                    "type": "fastq"
                }
            ],
            "position": {
                "left": 5040.296875,
                "top": 1349.00390625
            },
            "post_job_actions": {
                "TagDatasetActionoutput": {
                    "action_arguments": {
                        "tags": "p2_gfa,PurgedAlternateAssembly"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0",
            "tool_shed_repository": {
                "changeset_revision": "3ef480892a9f",
                "name": "gfastats",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mode_condition\": {\"selector\": \"manipulation\", \"__current_case__\": 0, \"swiss_army_knife\": {\"__class__\": \"ConnectedValue\"}, \"output_condition\": {\"out_format\": \"gfa\", \"__current_case__\": 4, \"terminal_overlaps_condition\": {\"terminal_overlaps_select\": \"yes\", \"__current_case__\": 1, \"terminal_overlaps_length\": \"500\"}}, \"discover_paths\": false, \"sort\": \"\", \"homopolymer_compress\": null}, \"target_condition\": {\"target_option\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.3.6+galaxy0",
            "type": "tool",
            "uuid": "f15eb7b7-c881-490b-8734-cc4d934eaa3a",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Purged Alternate assembly (gfa)",
                    "output_name": "output",
                    "uuid": "5323cc49-9368-44f9-b1db-e027bcc77abd"
                }
            ]
        },
        "39": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
            "errors": null,
            "id": 39,
            "input_connections": {
                "infile": {
                    "id": 35,
                    "output_name": "stats"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Text reformatting",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 5253.42578125,
                "top": 708.59765625
            },
            "post_job_actions": {
                "HideDatasetActionoutfile": {
                    "action_arguments": {},
                    "action_type": "HideDatasetAction",
                    "output_name": "outfile"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
            "tool_shed_repository": {
                "changeset_revision": "d698c222f354",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"code\": \"BEGIN{print \\\"Metric\\\\tAlternate\\\"}; {print}; \", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.1.2",
            "type": "tool",
            "uuid": "ed133b72-e945-4fe5-91d6-c71efa30678c",
            "when": null,
            "workflow_outputs": []
        },
        "40": {
            "annotation": "",
            "id": 40,
            "input_connections": {
                "gfa_stats": {
                    "id": 36,
                    "input_subworkflow_step_id": 0,
                    "output_name": "stats"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats_data_prep",
            "outputs": [],
            "position": {
                "left": 5760.26953125,
                "top": 526.87890625
            },
            "subworkflow": {
                "a_galaxy_workflow": "true",
                "annotation": "",
                "format-version": "0.1",
                "name": "gfastats_data_prep",
                "steps": {
                    "0": {
                        "annotation": "",
                        "content_id": null,
                        "errors": null,
                        "id": 0,
                        "input_connections": {},
                        "inputs": [
                            {
                                "description": "",
                                "name": "gfa_stats"
                            }
                        ],
                        "label": "gfa_stats",
                        "name": "Input dataset",
                        "outputs": [],
                        "position": {
                            "left": 0.0,
                            "top": 189.90056800842285
                        },
                        "tool_id": null,
                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                        "tool_version": null,
                        "type": "data_input",
                        "uuid": "56311775-399e-4e9e-aa48-8fa9fff12ad3",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "1": {
                        "annotation": "",
                        "content_id": "sort1",
                        "errors": null,
                        "id": 1,
                        "input_connections": {
                            "input": {
                                "id": 0,
                                "output_name": "output"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Sort",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 302.6136245727539,
                            "top": 0.0
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "sort1",
                        "tool_state": "{\"column\": \"2\", \"column_set\": [], \"header_lines\": \"0\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"order\": \"DESC\", \"style\": \"num\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.2.0",
                        "type": "tool",
                        "uuid": "7a31b528-ee29-4b2a-9270-6ae34ce198ef",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "2": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                        "errors": null,
                        "id": 2,
                        "input_connections": {
                            "infile": {
                                "id": 1,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Text reformatting",
                        "outputs": [
                            {
                                "name": "outfile",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 292.1306838989258,
                            "top": 235.1562442779541
                        },
                        "post_job_actions": {
                            "HideDatasetActionoutfile": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "outfile"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2",
                        "tool_shed_repository": {
                            "changeset_revision": "d698c222f354",
                            "name": "text_processing",
                            "owner": "bgruening",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"code\": \"{total += $2; $3 = total}1\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.1.2",
                        "type": "tool",
                        "uuid": "1a29dcd8-0ecd-4e4b-b7c4-ba688290eef3",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "3": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
                        "errors": null,
                        "id": 3,
                        "input_connections": {
                            "in_file": {
                                "id": 2,
                                "output_name": "outfile"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Datamash",
                        "outputs": [
                            {
                                "name": "out_file",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 595.0994338989258,
                            "top": 116.0227222442627
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0",
                        "tool_shed_repository": {
                            "changeset_revision": "4c07ddedc198",
                            "name": "datamash_ops",
                            "owner": "iuc",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"grouping\": \"\", \"header_in\": false, \"header_out\": false, \"ignore_case\": false, \"in_file\": {\"__class__\": \"ConnectedValue\"}, \"narm\": false, \"need_sort\": false, \"operations\": [{\"__index__\": 0, \"op_name\": \"absmax\", \"op_column\": \"3\"}], \"print_full_line\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.8+galaxy0",
                        "type": "tool",
                        "uuid": "053d0561-98e5-46b2-b554-685802fdb0ed",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "4": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "errors": null,
                        "id": 4,
                        "input_connections": {
                            "input": {
                                "id": 2,
                                "output_name": "outfile"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Add column",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 479.0482864379883,
                            "top": 456.17896461486816
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "tool_shed_repository": {
                            "changeset_revision": "023f0a3760b3",
                            "name": "add_value",
                            "owner": "devteam",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.0.1",
                        "type": "tool",
                        "uuid": "3b744e29-af55-4a10-9e56-bb637456ef54",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "5": {
                        "annotation": "",
                        "content_id": "param_value_from_file",
                        "errors": null,
                        "id": 5,
                        "input_connections": {
                            "input1": {
                                "id": 3,
                                "output_name": "out_file"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Parse parameter value",
                        "outputs": [
                            {
                                "name": "integer_param",
                                "type": "expression.json"
                            }
                        ],
                        "position": {
                            "left": 693.4658889770508,
                            "top": 299.4318027496338
                        },
                        "post_job_actions": {
                            "HideDatasetActioninteger_param": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "integer_param"
                            }
                        },
                        "tool_id": "param_value_from_file",
                        "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"integer\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "0.1.0",
                        "type": "tool",
                        "uuid": "b66fba8c-0e58-44ae-97eb-38fa3b408904",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "6": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
                        "errors": null,
                        "id": 6,
                        "input_connections": {
                            "components_1|param_type|component_value": {
                                "id": 5,
                                "output_name": "integer_param"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Compose text parameter value",
                        "outputs": [
                            {
                                "name": "out1",
                                "type": "expression.json"
                            }
                        ],
                        "position": {
                            "left": 885.0994338989258,
                            "top": 493.36646461486816
                        },
                        "post_job_actions": {
                            "HideDatasetActionout1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1",
                        "tool_shed_repository": {
                            "changeset_revision": "e188c9826e0f",
                            "name": "compose_text_param",
                            "owner": "iuc",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": \"c3/\"}}, {\"__index__\": 1, \"param_type\": {\"select_param_type\": \"integer\", \"__current_case__\": 1, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "0.1.1",
                        "type": "tool",
                        "uuid": "0477114d-32f5-4560-a3c5-3995c4cd8469",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "7": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
                        "errors": null,
                        "id": 7,
                        "input_connections": {
                            "input": {
                                "id": 4,
                                "output_name": "out_file1"
                            },
                            "ops|expressions_0|cond": {
                                "id": 6,
                                "output_name": "out1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Compute",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 1115.0993728637695,
                            "top": 735.5255222320557
                        },
                        "post_job_actions": {
                            "RenameDatasetActionout_file1": {
                                "action_arguments": {
                                    "newname": "gfastats data for plotting"
                                },
                                "action_type": "RenameDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0",
                        "tool_shed_repository": {
                            "changeset_revision": "6595517c2dd8",
                            "name": "column_maker",
                            "owner": "devteam",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"avoid_scientific_notation\": false, \"error_handling\": {\"auto_col_types\": true, \"fail_on_non_existent_columns\": true, \"non_computable\": {\"action\": \"--fail-on-non-computable\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"ops\": {\"header_lines_select\": \"no\", \"__current_case__\": 0, \"expressions\": [{\"__index__\": 0, \"cond\": {\"__class__\": \"ConnectedValue\"}, \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 1, \"cond\": \"c2/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}, {\"__index__\": 2, \"cond\": \"c3/1000000\", \"add_column\": {\"mode\": \"\", \"__current_case__\": 0, \"pos\": \"\"}}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "2.0",
                        "type": "tool",
                        "uuid": "602d39d3-ab8c-4f94-9119-f04ca5d2e750",
                        "when": null,
                        "workflow_outputs": [
                            {
                                "label": "gfastats data for plotting",
                                "output_name": "out_file1",
                                "uuid": "38ba0514-f27a-45fd-889b-5778f32e5ec6"
                            }
                        ]
                    }
                },
                "tags": "",
                "uuid": "897d85fa-c918-4698-a74b-af271762de1d"
            },
            "tool_id": null,
            "type": "subworkflow",
            "uuid": "71a56572-9780-41fd-a92a-9f306d93ac29",
            "when": null,
            "workflow_outputs": []
        },
        "41": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
            "errors": null,
            "id": 41,
            "input_connections": {
                "infile1": {
                    "id": 29,
                    "output_name": "outfile"
                },
                "infile2": {
                    "id": 39,
                    "output_name": "outfile"
                }
            },
            "inputs": [],
            "label": null,
            "name": "Join",
            "outputs": [
                {
                    "name": "output",
                    "type": "input"
                }
            ],
            "position": {
                "left": 5646.44140625,
                "top": 850.56640625
            },
            "post_job_actions": {
                "TagDatasetActionoutput": {
                    "action_arguments": {
                        "tags": "gfastats_p1_p2"
                    },
                    "action_type": "TagDatasetAction",
                    "output_name": "output"
                }
            },
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2",
            "tool_shed_repository": {
                "changeset_revision": "d698c222f354",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \"-a 1 -a 2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.1.2",
            "type": "tool",
            "uuid": "c620558f-324d-40cf-86b6-7460b52d49bf",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Assembly stats on Primary and alternate assemblies",
                    "output_name": "output",
                    "uuid": "36aaeacd-4752-43cb-9000-f859290c9ed2"
                }
            ]
        },
        "42": {
            "annotation": "",
            "id": 42,
            "input_connections": {
                "Alternate data": {
                    "id": 40,
                    "input_subworkflow_step_id": 1,
                    "output_name": "gfastats data for plotting"
                },
                "Name of alternate assembly": {
                    "id": 9,
                    "input_subworkflow_step_id": 3,
                    "output_name": "output"
                },
                "Name of primary assembly": {
                    "id": 8,
                    "input_subworkflow_step_id": 2,
                    "output_name": "output"
                },
                "Primary data": {
                    "id": 30,
                    "input_subworkflow_step_id": 0,
                    "output_name": "gfastats data for plotting"
                }
            },
            "inputs": [],
            "label": null,
            "name": "gfastats_plot",
            "outputs": [],
            "position": {
                "left": 6121.59765625,
                "top": 374.23828125
            },
            "subworkflow": {
                "a_galaxy_workflow": "true",
                "annotation": "",
                "creator": [
                    {
                        "class": "Organization",
                        "name": "Galaxy"
                    },
                    {
                        "class": "Organization",
                        "name": "VGP",
                        "url": "https://vertebrategenomeproject.org"
                    }
                ],
                "format-version": "0.1",
                "license": "CC-BY-4.0",
                "name": "gfastats_plot",
                "steps": {
                    "0": {
                        "annotation": "",
                        "content_id": null,
                        "errors": null,
                        "id": 0,
                        "input_connections": {},
                        "inputs": [
                            {
                                "description": "",
                                "name": "Primary data"
                            }
                        ],
                        "label": "Primary data",
                        "name": "Input dataset",
                        "outputs": [],
                        "position": {
                            "left": 0.0,
                            "top": 0.0
                        },
                        "tool_id": null,
                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                        "tool_version": null,
                        "type": "data_input",
                        "uuid": "bb14a035-f95c-4e8e-864a-6b69caad5a89",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "1": {
                        "annotation": "",
                        "content_id": null,
                        "errors": null,
                        "id": 1,
                        "input_connections": {},
                        "inputs": [
                            {
                                "description": "",
                                "name": "Alternate data"
                            }
                        ],
                        "label": "Alternate data",
                        "name": "Input dataset",
                        "outputs": [],
                        "position": {
                            "left": 6.960205078125,
                            "top": 143.53692626953125
                        },
                        "tool_id": null,
                        "tool_state": "{\"optional\": false, \"tag\": \"\"}",
                        "tool_version": null,
                        "type": "data_input",
                        "uuid": "262f039f-40c5-41c2-a36d-adcb840aea19",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "2": {
                        "annotation": "",
                        "content_id": null,
                        "errors": null,
                        "id": 2,
                        "input_connections": {},
                        "inputs": [
                            {
                                "description": "",
                                "name": "Name of primary assembly"
                            }
                        ],
                        "label": "Name of primary assembly",
                        "name": "Input parameter",
                        "outputs": [],
                        "position": {
                            "left": 4.55963134765625,
                            "top": 296.3210144042969
                        },
                        "tool_id": null,
                        "tool_state": "{\"default\": \"Primary\", \"parameter_type\": \"text\", \"optional\": true}",
                        "tool_version": null,
                        "type": "parameter_input",
                        "uuid": "1e24b121-b6e3-4478-b8c4-badfb50cf30e",
                        "when": null,
                        "workflow_outputs": [
                            {
                                "label": null,
                                "output_name": "output",
                                "uuid": "74a3fc5f-212c-43d5-adc2-103f490fa766"
                            }
                        ]
                    },
                    "3": {
                        "annotation": "",
                        "content_id": null,
                        "errors": null,
                        "id": 3,
                        "input_connections": {},
                        "inputs": [
                            {
                                "description": "",
                                "name": "Name of alternate assembly"
                            }
                        ],
                        "label": "Name of alternate assembly",
                        "name": "Input parameter",
                        "outputs": [],
                        "position": {
                            "left": 7.428955078125,
                            "top": 440.4403076171875
                        },
                        "tool_id": null,
                        "tool_state": "{\"default\": \"Alternate\", \"parameter_type\": \"text\", \"optional\": true}",
                        "tool_version": null,
                        "type": "parameter_input",
                        "uuid": "c2411d50-9786-4ff3-b316-5d60334dc340",
                        "when": null,
                        "workflow_outputs": [
                            {
                                "label": null,
                                "output_name": "output",
                                "uuid": "b886bb65-a905-4e2c-b6de-ae3dcc3749d7"
                            }
                        ]
                    },
                    "4": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "errors": null,
                        "id": 4,
                        "input_connections": {
                            "exp": {
                                "id": 2,
                                "output_name": "output"
                            },
                            "input": {
                                "id": 0,
                                "output_name": "output"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Add column",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 1139.7584686279297,
                            "top": 107.42897033691406
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "tool_shed_repository": {
                            "changeset_revision": "023f0a3760b3",
                            "name": "add_value",
                            "owner": "devteam",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"exp\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.0.1",
                        "type": "tool",
                        "uuid": "0fde4e58-dadf-4c75-8231-d5c838c05710",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "5": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "errors": null,
                        "id": 5,
                        "input_connections": {
                            "exp": {
                                "id": 3,
                                "output_name": "output"
                            },
                            "input": {
                                "id": 1,
                                "output_name": "output"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Add column",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 1151.7044982910156,
                            "top": 392.65625
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1",
                        "tool_shed_repository": {
                            "changeset_revision": "023f0a3760b3",
                            "name": "add_value",
                            "owner": "devteam",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"exp\": {\"__class__\": \"ConnectedValue\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"no\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.0.1",
                        "type": "tool",
                        "uuid": "f8602bb7-6924-4b52-932b-b862f5698ae0",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "6": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                        "errors": null,
                        "id": 6,
                        "input_connections": {
                            "inputs": {
                                "id": 4,
                                "output_name": "out_file1"
                            },
                            "queries_0|inputs2": {
                                "id": 5,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Concatenate datasets",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "input"
                            }
                        ],
                        "position": {
                            "left": 1441.193115234375,
                            "top": 216.59091186523438
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1",
                        "tool_shed_repository": {
                            "changeset_revision": "d698c222f354",
                            "name": "text_processing",
                            "owner": "bgruening",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [{\"__index__\": 0, \"inputs2\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "0.1.1",
                        "type": "tool",
                        "uuid": "a2dc3c75-6398-4a22-bbd1-254fa1112764",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "7": {
                        "annotation": "",
                        "content_id": "Cut1",
                        "errors": null,
                        "id": 7,
                        "input_connections": {
                            "input": {
                                "id": 6,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Cut",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "tabular"
                            }
                        ],
                        "position": {
                            "left": 1780.3265991210938,
                            "top": 182.99716186523438
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "Cut1",
                        "tool_state": "{\"columnList\": \"c8,c5,c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.0.2",
                        "type": "tool",
                        "uuid": "fc421b7d-5c43-4bef-8904-b08a79f517e6",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "8": {
                        "annotation": "",
                        "content_id": "Cut1",
                        "errors": null,
                        "id": 8,
                        "input_connections": {
                            "input": {
                                "id": 6,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": null,
                        "name": "Cut",
                        "outputs": [
                            {
                                "name": "out_file1",
                                "type": "tabular"
                            }
                        ],
                        "position": {
                            "left": 1781.349365234375,
                            "top": 387.96875
                        },
                        "post_job_actions": {
                            "HideDatasetActionout_file1": {
                                "action_arguments": {},
                                "action_type": "HideDatasetAction",
                                "output_name": "out_file1"
                            }
                        },
                        "tool_id": "Cut1",
                        "tool_state": "{\"columnList\": \"c8,c4,c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "1.0.2",
                        "type": "tool",
                        "uuid": "91e26e50-21d0-4380-bf84-a5bacef80541",
                        "when": null,
                        "workflow_outputs": []
                    },
                    "9": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1",
                        "errors": null,
                        "id": 9,
                        "input_connections": {
                            "input1": {
                                "id": 7,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": "Nx Plot",
                        "name": "Scatterplot with ggplot2",
                        "outputs": [
                            {
                                "name": "output1",
                                "type": "png"
                            }
                        ],
                        "position": {
                            "left": 2068.1390991210938,
                            "top": 31.988632202148438
                        },
                        "post_job_actions": {
                            "RenameDatasetActionoutput1": {
                                "action_arguments": {
                                    "newname": "Nx Plot"
                                },
                                "action_type": "RenameDatasetAction",
                                "output_name": "output1"
                            },
                            "TagDatasetActionoutput1": {
                                "action_arguments": {
                                    "tags": "#nx_plot"
                                },
                                "action_type": "TagDatasetAction",
                                "output_name": "output1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1",
                        "tool_shed_repository": {
                            "changeset_revision": "3b12bf9b4b87",
                            "name": "ggplot2_point",
                            "owner": "iuc",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"x\", \"xplot\": \"2\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "3.4.0+galaxy1",
                        "type": "tool",
                        "uuid": "80c6d25c-25e8-41dd-9f73-10aeda771d1d",
                        "when": null,
                        "workflow_outputs": [
                            {
                                "label": "Nx Plot",
                                "output_name": "output1",
                                "uuid": "10ea479b-6055-4295-ab4d-b4a3448ba241"
                            }
                        ]
                    },
                    "10": {
                        "annotation": "",
                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1",
                        "errors": null,
                        "id": 10,
                        "input_connections": {
                            "input1": {
                                "id": 8,
                                "output_name": "out_file1"
                            }
                        },
                        "inputs": [],
                        "label": "Size Plot",
                        "name": "Scatterplot with ggplot2",
                        "outputs": [
                            {
                                "name": "output1",
                                "type": "png"
                            }
                        ],
                        "position": {
                            "left": 2083.3805541992188,
                            "top": 319.8011169433594
                        },
                        "post_job_actions": {
                            "RenameDatasetActionoutput1": {
                                "action_arguments": {
                                    "newname": "Size Plot"
                                },
                                "action_type": "RenameDatasetAction",
                                "output_name": "output1"
                            },
                            "TagDatasetActionoutput1": {
                                "action_arguments": {
                                    "tags": "#size_plot"
                                },
                                "action_type": "TagDatasetAction",
                                "output_name": "output1"
                            }
                        },
                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1",
                        "tool_shed_repository": {
                            "changeset_revision": "3b12bf9b4b87",
                            "name": "ggplot2_point",
                            "owner": "iuc",
                            "tool_shed": "toolshed.g2.bx.psu.edu"
                        },
                        "tool_state": "{\"adv\": {\"type_conditional\": {\"type_options\": \"lines\", \"__current_case__\": 2}, \"factor\": {\"factoring\": \"Single\", \"__current_case__\": 1, \"factorcol\": \"1\", \"colors\": \"Set1\", \"colororder\": \"1\"}, \"axis_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"axis_text_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"plot_title_customization\": {\"axis_customization\": \"default\", \"__current_case__\": 0}, \"gridlinecust\": \"default\", \"transform\": \"none\", \"scaling\": {\"plot_scaling\": \"Automatic\", \"__current_case__\": 0}, \"theme\": \"bw\", \"legend\": \"yes\"}, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out\": {\"unit_output_dim\": \"in\", \"width_output_dim\": \"6.0\", \"height_output_dim\": \"4.0\", \"dpi_output_dim\": \"300.0\", \"additional_output_format\": \"none\"}, \"title\": \"\", \"xlab\": \"Scaffold number\", \"xplot\": \"2\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
                        "tool_version": "3.4.0+galaxy1",
                        "type": "tool",
                        "uuid": "d8440c79-e959-4f80-95ad-4b903c987979",
                        "when": null,
                        "workflow_outputs": [
                            {
                                "label": "Size Plot",
                                "output_name": "output1",
                                "uuid": "59e0d92b-8e0f-4e97-b6be-8656f1721abf"
                            }
                        ]
                    }
                },
                "tags": "",
                "uuid": "43d9a01f-b749-4f74-86a2-96a528e5a35b"
            },
            "tool_id": null,
            "type": "subworkflow",
            "uuid": "78a19ed6-ca17-4b55-9822-bd7bb42a4b22",
            "when": null,
            "workflow_outputs": [
                {
                    "label": "Nx Plot",
                    "output_name": "Nx Plot",
                    "uuid": "a15bf8fc-7eae-497b-9f75-ddaf474ade51"
                },
                {
                    "label": "Size Plot",
                    "output_name": "Size Plot",
                    "uuid": "b5516866-8b4f-41b8-a19a-12e1362d344c"
                }
            ]
        }
    },
    "tags": [
        "VGP_curated"
    ],
    "uuid": "a6c2fa10-d553-47a1-813f-12173d435709",
    "version": 4
}