{ "a_galaxy_workflow": "true", "annotation": "Scaffolding using HiC data with YAHS.", "creator": [ { "class": "Organization", "name": "VGP", "url": "https://vertebrategenomeproject.org" }, { "class": "Organization", "name": "Galaxy" } ], "format-version": "0.1", "license": "CC-BY-4.0", "release": "0.2", "name": "Scaffolding-HiC-VGP8", "steps": { "0": { "annotation": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. \n", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "The input GFA must conform to gfa1.2 standards, i.e. should have 'P' lines defined. Output GFAs from assemblers can be run through a GFA->GFA conversion using gfastats to ensure this. \n", "name": "Input GFA" } ], "label": "Input GFA", "name": "Input dataset", "outputs": [], "position": { "left": 0, "top": 163.55078125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "0c6a3af4-d5fc-442d-abc2-dc28c043abad", "when": null, "workflow_outputs": [] }, "1": { "annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "Sequence graph" } ], "label": "Sequence graph", "name": "Input dataset", "outputs": [], "position": { "left": 2.48046875, "top": 320.09375 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "6b5dfbf0-36da-4489-9f50-23c55ae5762f", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "4a853203-87b2-4ed0-b300-731e7a1aaff1" } ] }, "2": { "annotation": "Taxonomic lineage for the organism being assembled for Busco analysis\n", "content_id": null, "errors": null, "id": 2, "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": 89.68318337500133, "top": 487.5 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "e76f50b3-d497-4f51-884c-0dc181592f8f", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "cb5e2420-90a2-4609-8e4d-d3b0ef520376" } ] }, "3": { "annotation": "Forward reads as a single dataset in fastq format", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { "description": "Forward reads as a single dataset in fastq format", "name": "HiC Forward reads" } ], "label": "HiC Forward reads", "name": "Input dataset", "outputs": [], "position": { "left": 86.05427712500133, "top": 566.625 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "89a3dfc3-42c4-4c08-a221-7f3f844af0a4", "when": null, "workflow_outputs": [] }, "4": { "annotation": "Reverse reads as a single dataset in fastq format", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { "description": "Reverse reads as a single dataset in fastq format", "name": "HiC reverse reads" } ], "label": "HiC reverse reads", "name": "Input dataset", "outputs": [], "position": { "left": 86.54255837500133, "top": 673.9453125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"fastqsanger\", \"fastqsanger.gz\"], \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "3128533f-206a-41f0-9911-98b88e4f8714", "when": null, "workflow_outputs": [] }, "5": { "annotation": "Restriction enzymes used in preparation of Hi-C libraries.", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [ { "description": "Restriction enzymes used in preparation of Hi-C libraries.", "name": "Restriction enzymes" } ], "label": "Restriction enzymes", "name": "Input parameter", "outputs": [], "position": { "left": 95.12778237364729, "top": 786.2561485229093 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", "uuid": "68e8d6b9-f48f-4c78-a603-0623af75111e", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "2fc1e833-68f1-42d7-8246-55119940d36d" } ] }, "6": { "annotation": "Estimated genome size from contiging workflow", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { "description": "Estimated genome size from contiging workflow", "name": "Estimated genome size - Parameter File" } ], "label": "Estimated genome size - Parameter File", "name": "Input dataset", "outputs": [], "position": { "left": 112.3863140301566, "top": 915.1585681126172 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"estimated_genome_size\"}", "tool_version": null, "type": "data_input", "uuid": "b9768cf7-430a-4465-adc8-45497954f036", "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": 123.13630837500133, "top": 1019.3125 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, "type": "data_input", "uuid": "6067a21b-a403-4fef-9c9a-184b219a2924", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "7c1d63c8-8d07-48b8-875c-f649c7b1d9d7" } ] }, "8": { "annotation": "", "content_id": "param_value_from_file", "errors": null, "id": 8, "input_connections": { "input1": { "id": 6, "output_name": "output" } }, "inputs": [], "label": null, "name": "Parse parameter value", "outputs": [ { "name": "integer_param", "type": "expression.json" } ], "position": { "left": 2604.859933120587, "top": 1694.171875 }, "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": "8429fbf7-96d5-4b20-b90a-b794792c26c5", "when": null, "workflow_outputs": [] }, "9": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, "id": 9, "input_connections": { "input_file": { "id": 0, "output_name": "output" }, "mode_condition|swiss_army_knife": { "id": 7, "output_name": "output" } }, "inputs": [], "label": null, "name": "gfastats", "outputs": [ { "name": "output", "type": "fastq" } ], "position": { "left": 375.7027587890625, "top": 20.10939582812449 }, "post_job_actions": {}, "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\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"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": "be611894-245f-4d56-8622-7a457d85f478", "when": null, "workflow_outputs": [] }, "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, "id": 10, "input_connections": { "fastq_input|fastq_input1": { "id": 3, "output_name": "output" }, "reference_source|ref_file": { "id": 9, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool BWA-MEM2", "name": "fastq_input" }, { "description": "runtime parameter for tool BWA-MEM2", "name": "reference_source" } ], "label": null, "name": "BWA-MEM2", "outputs": [ { "name": "bam_output", "type": "bam" } ], "position": { "left": 1457.9766031901042, "top": 515.8124593098959 }, "post_job_actions": { "HideDatasetActionbam_output": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "bam_output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "tool_shed_repository": { "changeset_revision": "bfaa0d22c2e4", "name": "bwa_mem2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"output_sort\": \"name\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", "uuid": "1c192fd2-daba-46ad-8b98-4ab0bf1404ba", "when": null, "workflow_outputs": [] }, "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, "id": 11, "input_connections": { "fastq_input|fastq_input1": { "id": 4, "output_name": "output" }, "reference_source|ref_file": { "id": 9, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool BWA-MEM2", "name": "fastq_input" }, { "description": "runtime parameter for tool BWA-MEM2", "name": "reference_source" } ], "label": null, "name": "BWA-MEM2", "outputs": [ { "name": "bam_output", "type": "bam" } ], "position": { "left": 1367.45654296875, "top": 956.0625208281244 }, "post_job_actions": { "HideDatasetActionbam_output": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "bam_output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "tool_shed_repository": { "changeset_revision": "bfaa0d22c2e4", "name": "bwa_mem2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"output_sort\": \"name\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", "uuid": "5ea17098-2a3b-4fba-a2e1-4e3a8c4430ab", "when": null, "workflow_outputs": [] }, "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "errors": null, "id": 12, "input_connections": { "forward": { "id": 10, "output_name": "bam_output" }, "reverse": { "id": 11, "output_name": "bam_output" } }, "inputs": [], "label": null, "name": "Filter and merge", "outputs": [ { "name": "outfile", "type": "bam" } ], "position": { "left": 1700.3286831205874, "top": 753.28125 }, "post_job_actions": { "TagDatasetActionoutfile": { "action_arguments": { "tags": "merged_alignments_s1" }, "action_type": "TagDatasetAction", "output_name": "outfile" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "tool_shed_repository": { "changeset_revision": "321347bd0494", "name": "bellerophon", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"forward\": {\"__class__\": \"ConnectedValue\"}, \"quality\": \"20\", \"reverse\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0+galaxy1", "type": "tool", "uuid": "e7b502ef-c2a7-4b14-b4fe-d88938577974", "when": null, "workflow_outputs": [] }, "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", "errors": null, "id": 13, "input_connections": { "input": { "id": 12, "output_name": "outfile" } }, "inputs": [], "label": null, "name": "PretextMap", "outputs": [ { "name": "pretext_map_out", "type": "pretext" } ], "position": { "left": 1958.5879278674058, "top": 981.2891393226516 }, "post_job_actions": { "TagDatasetActionpretext_map_out": { "action_arguments": { "tags": "pretextmap_s1, #s1" }, "action_type": "TagDatasetAction", "output_name": "pretext_map_out" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", "tool_shed_repository": { "changeset_revision": "dfb8a4497339", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": null, \"sorting\": {\"sortby\": \"nosort\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.9+galaxy0", "type": "tool", "uuid": "6d280ad6-6803-44c3-8afe-5b5ff424c98d", "when": null, "workflow_outputs": [] }, "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1", "errors": null, "id": 14, "input_connections": { "function|agp": { "id": 1, "output_name": "output" }, "function|bfile": { "id": 12, "output_name": "outfile" }, "function|enzyme_conditional|preconfigured_enzymes": { "id": 5, "output_name": "output" }, "function|fasta": { "id": 9, "output_name": "output" } }, "inputs": [], "label": null, "name": "YAHS", "outputs": [ { "name": "initial_agp_break", "type": "input" }, { "name": "agp_break", "type": "input" }, { "name": "agp_out", "type": "input" }, { "name": "final_agp_out", "type": "agp" }, { "name": "final_fasta_out", "type": "fasta" }, { "name": "log_file", "type": "txt" } ], "position": { "left": 2484.703683120587, "top": 0 }, "post_job_actions": { "TagDatasetActionfinal_agp_out": { "action_arguments": { "tags": "s2_agp, #s2" }, "action_type": "TagDatasetAction", "output_name": "final_agp_out" }, "TagDatasetActionfinal_fasta_out": { "action_arguments": { "tags": "s2_fasta, #s2" }, "action_type": "TagDatasetAction", "output_name": "final_fasta_out" }, "TagDatasetActionlog_file": { "action_arguments": { "tags": "s2_log, #s2" }, "action_type": "TagDatasetAction", "output_name": "log_file" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/yahs/yahs/1.2a.2+galaxy1", "tool_shed_repository": { "changeset_revision": "425e63adcc5d", "name": "yahs", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"function\": {\"function_select\": \"yahs\", \"__current_case__\": 0, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"bfile\": {\"__class__\": \"ConnectedValue\"}, \"agp\": {\"__class__\": \"ConnectedValue\"}, \"res\": \"\", \"enzyme_conditional\": {\"enzyme_options\": \"preconfigured\", \"__current_case__\": 1, \"preconfigured_enzymes\": {\"__class__\": \"ConnectedValue\"}}, \"length\": null, \"quality\": null, \"no_contig_ec\": true, \"no_scaffold_ec\": false}, \"log_out\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.2a.2+galaxy1", "type": "tool", "uuid": "204fe2a0-4486-4dde-90b1-560aa909eb33", "when": null, "workflow_outputs": [ { "label": "YAHS on input dataset(s): Final scaffolds agp output", "output_name": "final_agp_out", "uuid": "8f9d422b-3f0f-47f4-a1f3-d957a5f49118" } ] }, "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, "id": 15, "input_connections": { "input": { "id": 13, "output_name": "pretext_map_out" } }, "inputs": [], "label": null, "name": "Pretext Snapshot", "outputs": [ { "name": "pretext_snap_out", "type": "input" } ], "position": { "left": 2228.703683120587, "top": 971.375 }, "post_job_actions": { "HideDatasetActionpretext_snap_out": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "pretext_snap_out" }, "TagDatasetActionpretext_snap_out": { "action_arguments": { "tags": "pretext_s1" }, "action_type": "TagDatasetAction", "output_name": "pretext_snap_out" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "tool_shed_repository": { "changeset_revision": "44c66e8d21e6", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.3+galaxy1", "type": "tool", "uuid": "ad7305d0-d613-4203-8ae8-d8ca469eddd5", "when": null, "workflow_outputs": [] }, "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, "id": 16, "input_connections": { "input_file": { "id": 9, "output_name": "output" }, "mode_condition|agp_to_path": { "id": 14, "output_name": "final_agp_out" } }, "inputs": [], "label": null, "name": "gfastats", "outputs": [ { "name": "output", "type": "fastq" } ], "position": { "left": 2827.99169921875, "top": 128.21483406054637 }, "post_job_actions": { "RenameDatasetActionoutput": { "action_arguments": { "newname": "Reconciliated Scaffolds: gfa" }, "action_type": "RenameDatasetAction", "output_name": "output" }, "TagDatasetActionoutput": { "action_arguments": { "tags": "s2_gfa" }, "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\": \"scaffolding\", \"__current_case__\": 2, \"agp_to_path\": {\"__class__\": \"ConnectedValue\"}, \"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": "95290218-32e1-4466-9511-e9822154d3dd", "when": null, "workflow_outputs": [ { "label": "Reconciliated Scaffolds: gfa", "output_name": "output", "uuid": "671d3d09-a7ab-496c-a3a1-3b3fe8675ffd" } ] }, "17": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, "id": 17, "input_connections": { "input": { "id": 15, "output_name": "pretext_snap_out" } }, "inputs": [], "label": null, "name": "Extract dataset", "outputs": [ { "name": "output", "type": "data" } ], "position": { "left": 2598.922433120587, "top": 1090.8125 }, "post_job_actions": { "TagDatasetActionoutput": { "action_arguments": { "tags": "pretext_s1" }, "action_type": "TagDatasetAction", "output_name": "output" } }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"first\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "uuid": "081cea0b-17fd-49f1-8774-c6a5029e7a5b", "when": null, "workflow_outputs": [ { "label": "Pretext Map Before HiC scaffolding", "output_name": "output", "uuid": "f6f4e543-5204-43c8-b867-62775fc8cea5" } ] }, "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, "id": 18, "input_connections": { "input_file": { "id": 16, "output_name": "output" }, "mode_condition|swiss_army_knife": { "id": 7, "output_name": "output" } }, "inputs": [], "label": null, "name": "gfastats", "outputs": [ { "name": "output", "type": "fastq" } ], "position": { "left": 3252.188058120587, "top": 324.421875 }, "post_job_actions": { "TagDatasetActionoutput": { "action_arguments": { "tags": "s2_fasta" }, "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\": \"fasta\", \"__current_case__\": 0, \"line_length\": null}, \"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": "38257089-cca2-46d0-9e44-322dceebec42", "when": null, "workflow_outputs": [ { "label": "Reconciliated Scaffolds: fasta", "output_name": "output", "uuid": "d1a62645-80b0-4939-baa6-f3fcf982085e" } ] }, "19": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, "id": 19, "input_connections": { "input_file": { "id": 16, "output_name": "output" }, "mode_condition|statistics_condition|expected_genomesize": { "id": 8, "output_name": "integer_param" } }, "inputs": [], "label": null, "name": "gfastats", "outputs": [ { "name": "stats", "type": "tabular" } ], "position": { "left": 3711.719308120587, "top": 1761.203125 }, "post_job_actions": { "TagDatasetActionstats": { "action_arguments": { "tags": "gfastats_asm_s2, #s2" }, "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": "2207f3c6-a651-42ba-b6e7-350c9c6a2db7", "when": null, "workflow_outputs": [ { "label": "Assembly Statistics for s2", "output_name": "stats", "uuid": "ee8af1cd-1535-4f63-a17b-e57ca1cb47b3" } ] }, "20": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0", "errors": null, "id": 20, "input_connections": { "input_file": { "id": 16, "output_name": "output" } }, "inputs": [], "label": null, "name": "gfastats", "outputs": [ { "name": "stats", "type": "tabular" } ], "position": { "left": 3839.375558120587, "top": 1568.171875 }, "post_job_actions": { "TagDatasetActionstats": { "action_arguments": { "tags": "gfastats_scaffolds_s2, #s2" }, "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\": \"s\"}, \"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": "0fc8b3a2-550f-4891-aa05-a1cea35f0b5e", "when": null, "workflow_outputs": [ { "label": "Scaffold sizes for s2", "output_name": "stats", "uuid": "17e925f3-e890-4608-b9fb-b9b83b2a120a" } ] }, "21": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, "id": 21, "input_connections": { "fastq_input|fastq_input1": { "id": 3, "output_name": "output" }, "reference_source|ref_file": { "id": 18, "output_name": "output" } }, "inputs": [], "label": null, "name": "BWA-MEM2", "outputs": [ { "name": "bam_output", "type": "bam" } ], "position": { "left": 3499.078683120587, "top": 550.453125 }, "post_job_actions": { "HideDatasetActionbam_output": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "bam_output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "tool_shed_repository": { "changeset_revision": "bfaa0d22c2e4", "name": "bwa_mem2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"output_sort\": \"name\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", "uuid": "e68b1c36-8731-4c75-8f04-2eab2fad5f3e", "when": null, "workflow_outputs": [] }, "22": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "errors": null, "id": 22, "input_connections": { "fastq_input|fastq_input1": { "id": 4, "output_name": "output" }, "reference_source|ref_file": { "id": 18, "output_name": "output" } }, "inputs": [], "label": null, "name": "BWA-MEM2", "outputs": [ { "name": "bam_output", "type": "bam" } ], "position": { "left": 3497.922433120587, "top": 828.171875 }, "post_job_actions": { "HideDatasetActionbam_output": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "bam_output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bwa_mem2/bwa_mem2/2.2.1+galaxy1", "tool_shed_repository": { "changeset_revision": "bfaa0d22c2e4", "name": "bwa_mem2", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"analysis_type\": {\"analysis_type_selector\": \"illumina\", \"__current_case__\": 0}, \"fastq_input\": {\"fastq_input_selector\": \"single\", \"__current_case__\": 1, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}}, \"output_sort\": \"name\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}}, \"rg\": {\"rg_selector\": \"do_not_set\", \"__current_case__\": 3}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", "uuid": "62e9129f-bfd9-4583-8174-3459bd03729a", "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": 18, "output_name": "output" }, "lineage|lineage_dataset": { "id": 2, "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": 3784.714433375001, "top": 276.07421875 }, "post_job_actions": { "TagDatasetActionbusco_missing": { "action_arguments": { "tags": "busco_s2_missing" }, "action_type": "TagDatasetAction", "output_name": "busco_missing" }, "TagDatasetActionbusco_sum": { "action_arguments": { "tags": "busco_s2_summ" }, "action_type": "TagDatasetAction", "output_name": "busco_sum" }, "TagDatasetActionbusco_table": { "action_arguments": { "tags": " busco_s2_full" }, "action_type": "TagDatasetAction", "output_name": "busco_table" }, "TagDatasetActionsummary_image": { "action_arguments": { "tags": "busco_s2_img" }, "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": "9e1fe0cc-77a8-4239-a139-14900a5fcc94", "when": null, "workflow_outputs": [ { "label": "Busco Summary", "output_name": "busco_sum", "uuid": "b9937b4e-aed2-4fcf-aad2-1b56d65bed84" }, { "label": "Busco Summary image", "output_name": "summary_image", "uuid": "5e1fe01a-5d84-4deb-a30b-c2a2d4b46b61" } ] }, "24": { "annotation": "", "id": 24, "input_connections": { "gfa_stats": { "id": 20, "input_subworkflow_step_id": 0, "output_name": "stats" } }, "inputs": [], "label": null, "name": "gfastats_data_prep", "outputs": [], "position": { "left": 4372.234933120587, "top": 1677.609375 }, "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": "fdbf6b66-a9af-446d-bcfc-751cced346cd", "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": "f1b3bcb0-fdcb-4371-b290-fddd744ea5f5", "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": "dbb92d28-6ffc-446d-8c9e-af5b050312e0", "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": "b1ee0d01-e74a-4d7a-93c1-98c2b2df51e0", "when": null, "workflow_outputs": [] }, "4": { "annotation": "", "content_id": "addValue", "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": "addValue", "tool_state": "{\"exp\": \"1\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"iterate\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", "uuid": "6ec1a5cb-d2c5-4e83-a9cb-e6d0c848e65a", "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": "b11a26ab-1b2a-431d-9300-149d64a6fd4b", "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": "b33c8190-2050-4cb2-952b-14b6fb743871", "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": "c0c0c727-dd65-4c49-8a11-d9a478e6c12a", "when": null, "workflow_outputs": [ { "label": "gfastats data for plotting", "output_name": "out_file1", "uuid": "d246b00a-6e3b-4523-995c-04bfbf58a684" } ] } }, "tags": "", "uuid": "1302e300-2959-4af9-8532-e42bbba8aea4" }, "tool_id": null, "type": "subworkflow", "uuid": "83f9b620-0516-4c3f-b6fe-0897a8852440", "when": null, "workflow_outputs": [] }, "25": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "errors": null, "id": 25, "input_connections": { "forward": { "id": 21, "output_name": "bam_output" }, "reverse": { "id": 22, "output_name": "bam_output" } }, "inputs": [], "label": null, "name": "Filter and merge", "outputs": [ { "name": "outfile", "type": "bam" } ], "position": { "left": 3801.906808120587, "top": 827.390625 }, "post_job_actions": { "TagDatasetActionoutfile": { "action_arguments": { "tags": "merged_alignments_s2" }, "action_type": "TagDatasetAction", "output_name": "outfile" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bellerophon/bellerophon/1.0+galaxy1", "tool_shed_repository": { "changeset_revision": "321347bd0494", "name": "bellerophon", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"forward\": {\"__class__\": \"ConnectedValue\"}, \"quality\": \"20\", \"reverse\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0+galaxy1", "type": "tool", "uuid": "ba91283e-b942-44b4-89f3-acae2c64a614", "when": null, "workflow_outputs": [] }, "26": { "annotation": "", "content_id": "Cut1", "errors": null, "id": 26, "input_connections": { "input": { "id": 24, "output_name": "gfastats data for plotting" } }, "inputs": [], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 4935.641183120587, "top": 1404.421875 }, "post_job_actions": {}, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"c5,c6\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.2", "type": "tool", "uuid": "b6dad0fb-da2c-4834-bd1e-d50f93397d56", "when": null, "workflow_outputs": [] }, "27": { "annotation": "", "content_id": "Cut1", "errors": null, "id": 27, "input_connections": { "input": { "id": 24, "output_name": "gfastats data for plotting" } }, "inputs": [], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 4937.672433120587, "top": 1545.40625 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"c4,c7\", \"delimiter\": \"T\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.2", "type": "tool", "uuid": "857e88d4-43fb-4b2a-87fc-5beb5e5ae360", "when": null, "workflow_outputs": [] }, "28": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", "errors": null, "id": 28, "input_connections": { "input": { "id": 25, "output_name": "outfile" } }, "inputs": [], "label": null, "name": "PretextMap", "outputs": [ { "name": "pretext_map_out", "type": "pretext" } ], "position": { "left": 4140.766183120587, "top": 961.375 }, "post_job_actions": { "TagDatasetActionpretext_map_out": { "action_arguments": { "tags": "pretextmap_s2, #s2" }, "action_type": "TagDatasetAction", "output_name": "pretext_map_out" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_map/pretext_map/0.1.9+galaxy0", "tool_shed_repository": { "changeset_revision": "dfb8a4497339", "name": "pretext_map", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"filter\": {\"filter_type\": \"\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"map_qual\": null, \"sorting\": {\"sortby\": \"nosort\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.9+galaxy0", "type": "tool", "uuid": "2eebc19f-da4f-4ec2-8030-81f81cc38fdf", "when": null, "workflow_outputs": [] }, "29": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2", "errors": null, "id": 29, "input_connections": { "input": { "id": 25, "output_name": "outfile" } }, "inputs": [], "label": null, "name": "bedtools BAM to BED", "outputs": [ { "name": "output", "type": "bed" } ], "position": { "left": 4282.953683120587, "top": 721.03125 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2", "tool_shed_repository": { "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"ed_score\": false, \"input\": {\"__class__\": \"ConnectedValue\"}, \"option\": \"-bed12\", \"split\": false, \"tag\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.30.0+galaxy2", "type": "tool", "uuid": "7afcb308-39dd-4a22-b787-c751952777d4", "when": null, "workflow_outputs": [] }, "30": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, "id": 30, "input_connections": { "input1": { "id": 26, "output_name": "out_file1" } }, "inputs": [], "label": "Nx Plot", "name": "Scatterplot with ggplot2", "outputs": [ { "name": "output1", "type": "png" } ], "position": { "left": 5215.016183120587, "top": 1327.078125 }, "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\": \"Default\", \"__current_case__\": 0}, \"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\": \"1\", \"ylab\": \"Nx (Mb)\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "3.4.0+galaxy1", "type": "tool", "uuid": "a544c06c-ce84-4764-86a5-64156da53e70", "when": null, "workflow_outputs": [ { "label": "Nx Plot", "output_name": "output1", "uuid": "9228733c-40da-48e7-94ec-a0477bb350c5" } ] }, "31": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/3.4.0+galaxy1", "errors": null, "id": 31, "input_connections": { "input1": { "id": 27, "output_name": "out_file1" } }, "inputs": [], "label": "Size Plot", "name": "Scatterplot with ggplot2", "outputs": [ { "name": "output1", "type": "png" } ], "position": { "left": 5206.734933120587, "top": 1561.296875 }, "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\": \"Default\", \"__current_case__\": 0}, \"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\": \"1\", \"ylab\": \"Cumulative Size (Mb)\", \"yplot\": \"2\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "3.4.0+galaxy1", "type": "tool", "uuid": "4debf869-faae-49f1-8668-d9adcae2d92f", "when": null, "workflow_outputs": [ { "label": "Size Plot", "output_name": "output1", "uuid": "e4070c52-a085-40f6-9ea0-1098738d7bba" } ] }, "32": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "errors": null, "id": 32, "input_connections": { "input": { "id": 28, "output_name": "pretext_map_out" } }, "inputs": [], "label": null, "name": "Pretext Snapshot", "outputs": [ { "name": "pretext_snap_out", "type": "input" } ], "position": { "left": 4509.1334844570965, "top": 1064.8994221213547 }, "post_job_actions": { "HideDatasetActionpretext_snap_out": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "pretext_snap_out" }, "TagDatasetActionpretext_snap_out": { "action_arguments": { "tags": "pretext_s2" }, "action_type": "TagDatasetAction", "output_name": "pretext_snap_out" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pretext_snapshot/pretext_snapshot/0.0.3+galaxy1", "tool_shed_repository": { "changeset_revision": "44c66e8d21e6", "name": "pretext_snapshot", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"colormap\": \"5\", \"formats\": {\"outformat\": \"png\", \"__current_case__\": 0}, \"grid\": {\"showGrid\": true, \"__current_case__\": 0, \"gridsize\": \"1\", \"gridcolor\": \"black\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mintexels\": \"64\", \"resolution\": \"1000\", \"sequencenames\": false, \"sequences\": \"=full\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.0.3+galaxy1", "type": "tool", "uuid": "6e14e43c-ac36-499c-bf33-c513edd7445d", "when": null, "workflow_outputs": [] }, "33": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", "errors": null, "id": 33, "input_connections": { "infile": { "id": 29, "output_name": "output" } }, "inputs": [], "label": null, "name": "Sort", "outputs": [ { "name": "outfile", "type": "input" } ], "position": { "left": 4596.258316145335, "top": 390.1009386788954 }, "post_job_actions": { "TagDatasetActionoutfile": { "action_arguments": { "tags": "sorted_merged_alignments_s2" }, "action_type": "TagDatasetAction", "output_name": "outfile" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", "tool_shed_repository": { "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"header\": \"0\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"4\", \"order\": \"\", \"style\": \"\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.1", "type": "tool", "uuid": "1a3de58d-2ff9-48f1-a1d6-fab5d28f0b0b", "when": null, "workflow_outputs": [] }, "34": { "annotation": "", "content_id": "__EXTRACT_DATASET__", "errors": null, "id": 34, "input_connections": { "input": { "id": 32, "output_name": "pretext_snap_out" } }, "inputs": [], "label": null, "name": "Extract dataset", "outputs": [ { "name": "output", "type": "data" } ], "position": { "left": 4773.453683120587, "top": 1125.96875 }, "post_job_actions": { "TagDatasetActionoutput": { "action_arguments": { "tags": "pretext_s2" }, "action_type": "TagDatasetAction", "output_name": "output" } }, "tool_id": "__EXTRACT_DATASET__", "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"which\": {\"which_dataset\": \"first\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.1", "type": "tool", "uuid": "df9dfd34-8b01-4146-b2c4-3e5bfef08121", "when": null, "workflow_outputs": [ { "label": "Pretext Map After HiC scaffolding", "output_name": "output", "uuid": "c4d0b6de-445f-4e23-9ddd-04f3f54712da" } ] } }, "tags": [ "VGP_curated" ], "uuid": "434ddf40-c218-42d1-8c7b-a7c5fcd18736", "version": 14 }