{ "a_galaxy_workflow": "true", "annotation": "", "creator": [ { "class": "Organization", "name": "VGP", "url": "https://vertebrategenomeproject.org" }, { "class": "Organization", "name": "Galaxy" } ], "format-version": "0.1", "license": "CC-BY-4.0", "release":"0.1.4", "name": "kmer-profiling-hifi-VGP1", "steps": { "0": { "annotation": "A simple list collection containing PacBio data in either fastq or fasta format", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "A simple list collection containing PacBio data in either fastq or fasta format", "name": "Collection of Pacbio Data" } ], "label": "Collection of Pacbio Data", "name": "Input dataset collection", "outputs": [], "position": { "left": 0.0, "top": 86.5078125 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", "uuid": "861c3a49-1055-4030-9a91-e53cbf1ac436", "when": null, "workflow_outputs": [] }, "1": { "annotation": "", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "", "name": "K-mer length " } ], "label": "K-mer length ", "name": "Input parameter", "outputs": [], "position": { "left": 17.57421875, "top": 226.734375 }, "tool_id": null, "tool_state": "{\"default\": 21, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "946bcadd-8ab0-4595-9985-abb574539844", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "18b69ad3-4c09-46f5-9a4c-bf4097b37fef" } ] }, "2": { "annotation": "Ploidy for the organism being assembled", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { "description": "Ploidy for the organism being assembled", "name": "Ploidy" } ], "label": "Ploidy", "name": "Input parameter", "outputs": [], "position": { "left": 50.12890625, "top": 342.609375 }, "tool_id": null, "tool_state": "{\"default\": 2, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "e3848560-55a2-42a5-ac1a-487ccf084d92", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "1fea95fa-67d6-408d-94b6-264107cc19a1" } ] }, "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, "id": 3, "input_connections": { "operation_type|input_reads": { "id": 0, "output_name": "output" }, "operation_type|options_kmer_size|input_kmer_size": { "id": 1, "output_name": "output" } }, "inputs": [], "label": null, "name": "Meryl", "outputs": [ { "name": "read_db", "type": "meryldb" } ], "position": { "left": 296.8668759977911, "top": 27 }, "post_job_actions": { "HideDatasetActionread_db": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "read_db" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "tool_shed_repository": { "changeset_revision": "29dabd8db6f2", "name": "meryl", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"operation_type\": {\"command_type\": \"count-kmers\", \"__current_case__\": 0, \"count_operations\": \"count\", \"input_reads\": {\"__class__\": \"ConnectedValue\"}, \"options_kmer_size\": {\"kmer_size\": \"provide\", \"__current_case__\": 0, \"input_kmer_size\": {\"__class__\": \"ConnectedValue\"}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy6", "type": "tool", "uuid": "9f3718fe-c33a-43c1-b36e-964a929678f7", "when": null, "workflow_outputs": [] }, "4": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, "id": 4, "input_connections": { "operation_type|input_meryldb_02": { "id": 3, "output_name": "read_db" } }, "inputs": [], "label": null, "name": "Meryl", "outputs": [ { "name": "read_db", "type": "meryldb" } ], "position": { "left": 576.8668759977911, "top": 0 }, "post_job_actions": { "TagDatasetActionread_db": { "action_arguments": { "tags": "meryl_db,Meryl Database" }, "action_type": "TagDatasetAction", "output_name": "read_db" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "tool_shed_repository": { "changeset_revision": "29dabd8db6f2", "name": "meryl", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"operation_type\": {\"command_type\": \"groups-kmers\", \"__current_case__\": 3, \"groups_operations\": \"union-sum\", \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy6", "type": "tool", "uuid": "6467a6da-23e0-4ee0-af0e-7f5fc8a636de", "when": null, "workflow_outputs": [ { "label": "Merged Meryl Database", "output_name": "read_db", "uuid": "9055fdc0-d158-435e-b662-e5a4f2766b42" } ] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "errors": null, "id": 5, "input_connections": { "operation_type|input_meryldb_02": { "id": 4, "output_name": "read_db" } }, "inputs": [], "label": null, "name": "Meryl", "outputs": [ { "name": "read_db_hist", "type": "tabular" } ], "position": { "left": 856.8668759977911, "top": 42 }, "post_job_actions": { "HideDatasetActionread_db_hist": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "read_db_hist" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/meryl/meryl/1.3+galaxy6", "tool_shed_repository": { "changeset_revision": "29dabd8db6f2", "name": "meryl", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"operation_type\": {\"command_type\": \"histogram-kmers\", \"__current_case__\": 4, \"input_meryldb_02\": {\"__class__\": \"ConnectedValue\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.3+galaxy6", "type": "tool", "uuid": "10eb771d-1437-4602-91b7-e7e6d806dc2e", "when": null, "workflow_outputs": [] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", "errors": null, "id": 6, "input_connections": { "input": { "id": 5, "output_name": "read_db_hist" }, "kmer_length": { "id": 1, "output_name": "output" }, "ploidy": { "id": 2, "output_name": "output" } }, "inputs": [], "label": null, "name": "GenomeScope", "outputs": [ { "name": "linear_plot", "type": "png" }, { "name": "log_plot", "type": "png" }, { "name": "transformed_linear_plot", "type": "png" }, { "name": "transformed_log_plot", "type": "png" }, { "name": "model", "type": "txt" }, { "name": "summary", "type": "txt" }, { "name": "model_params", "type": "tabular" } ], "position": { "left": 1136.866875997791, "top": 15 }, "post_job_actions": { "TagDatasetActionlinear_plot": { "action_arguments": { "tags": "genomescope_linear,Linear Plot" }, "action_type": "TagDatasetAction", "output_name": "linear_plot" }, "TagDatasetActionlog_plot": { "action_arguments": { "tags": "genomescope_log,Log Plot" }, "action_type": "TagDatasetAction", "output_name": "log_plot" }, "TagDatasetActionmodel": { "action_arguments": { "tags": "genomescope_model" }, "action_type": "TagDatasetAction", "output_name": "model" }, "TagDatasetActionmodel_params": { "action_arguments": { "tags": "genomescope_params,GenomeScope Parameters" }, "action_type": "TagDatasetAction", "output_name": "model_params" }, "TagDatasetActionsummary": { "action_arguments": { "tags": "genomescope_summ,GenomeScope Summary" }, "action_type": "TagDatasetAction", "output_name": "summary" }, "TagDatasetActiontransformed_linear_plot": { "action_arguments": { "tags": "genomescope_tr_linear,Transformed Linear Plot" }, "action_type": "TagDatasetAction", "output_name": "transformed_linear_plot" }, "TagDatasetActiontransformed_log_plot": { "action_arguments": { "tags": "genomescope_tr_log,Transformed Log Plot" }, "action_type": "TagDatasetAction", "output_name": "transformed_log_plot" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/genomescope/genomescope/2.0+galaxy2", "tool_shed_repository": { "changeset_revision": "01210c4e9144", "name": "genomescope", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"advanced_options\": {\"topology\": null, \"initial_repetitiveness\": null, \"initial_heterozygosities\": \"\", \"transform_exp\": null, \"testing\": true, \"true_params\": \"\", \"trace_flag\": false, \"num_rounds\": null}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"kmer_length\": {\"__class__\": \"ConnectedValue\"}, \"lambda\": null, \"max_kmercov\": null, \"output_options\": {\"output_files\": [\"model_output\", \"summary_output\"], \"no_unique_sequence\": false}, \"ploidy\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.0+galaxy2", "type": "tool", "uuid": "955de351-ef19-42dc-89d7-ca213994515a", "when": null, "workflow_outputs": [ { "label": "GenomeScope linear plot", "output_name": "linear_plot", "uuid": "57230be4-36d5-4307-b4b0-b8a73f6800ce" }, { "label": "GenomeScope transformed linear plot", "output_name": "transformed_linear_plot", "uuid": "48e2c4c5-8658-44e6-8981-673a2f1f719e" }, { "label": "GenomeScope transformed log plot", "output_name": "transformed_log_plot", "uuid": "ea87bd08-a6d9-4c9e-9497-8bfb1725da04" }, { "label": "GenomeScope summary", "output_name": "summary", "uuid": "b74004e1-4f4b-4f43-a9f0-2a7a0a70ca1d" }, { "label": "GenomeScope Model Parameters", "output_name": "model_params", "uuid": "cb88b945-413c-4e2d-81a9-dd838df902ff" }, { "label": "GenomeScope log plot", "output_name": "log_plot", "uuid": "988e2189-d5f2-4e9e-8fc2-4434e68e8501" } ] } }, "tags": [ "Reviewed", "VGP" ], "uuid": "7542ffba-d083-415e-b745-08d9503debc4", "version": 4 }