Mercurial > repos > earlhaminst > geneseqtofamily
view finding_orphan_genes.ga @ 1:267a94f068d7 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 424b04f764977420ce4d92ebee5929fa18a30efb-dirty
author | earlhaminst |
---|---|
date | Mon, 20 Feb 2017 12:57:16 -0500 |
parents | b92f5ab6d127 |
children |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "Orphan genes", "steps": { "0": { "annotation": "Output file from blast_parser of GeneSeqToFamily", "content_id": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "Output file from blast_parser of GeneSeqToFamily", "name": "blast_parser data" } ], "label": "blast_parser data", "name": "Input dataset", "outputs": [], "position": { "left": 199.9375, "top": 276.4375 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"blast_parser data\"}", "tool_version": null, "type": "data_input", "uuid": "f8f73cb1-7472-44e6-9bd6-40dd0f2103d0", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "197d2b5b-2790-4eb8-be7d-f2ee15165b2a" } ] }, "1": { "annotation": "Same CDS, used to run BLASTP in GeneSeqToFamily", "content_id": null, "id": 1, "input_connections": {}, "inputs": [ { "description": "Same CDS, used to run BLASTP in GeneSeqToFamily", "name": "CDS" } ], "label": "CDS", "name": "Input dataset", "outputs": [], "position": { "left": 195.921875, "top": 553.359375 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"CDS\"}", "tool_version": null, "type": "data_input", "uuid": "2856205c-2a2b-4f2a-a177-2bfc78352840", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "5e46019a-f8fb-4507-8206-2402d8088ca5" } ] }, "2": { "annotation": "List of IDs discarded from hcluster_sg results", "content_id": null, "id": 2, "input_connections": {}, "inputs": [ { "description": "List of IDs discarded from hcluster_sg results", "name": "hcluster_sg discarded" } ], "label": "hcluster_sg discarded", "name": "Input dataset", "outputs": [], "position": { "left": 191, "top": 697 }, "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"hcluster_sg discarded\"}", "tool_version": null, "type": "data_input", "uuid": "3866a37f-3309-4c5d-8ed9-bb7c21d25d8a", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "f9fe709d-8a1b-44b0-9989-688af44b16ad" } ] }, "3": { "annotation": "", "content_id": "Cut1", "id": 3, "input_connections": { "input": { "id": 0, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Cut", "name": "input" } ], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 429.953125, "top": 276.4375 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.2", "type": "tool", "uuid": "3d809485-291c-4858-ade6-2f465bf667f0", "workflow_outputs": [] }, "4": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0", "id": 4, "input_connections": { "input": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool FASTA-to-Tabular", "name": "input" } ], "label": null, "name": "FASTA-to-Tabular", "outputs": [ { "name": "output", "type": "tabular" } ], "position": { "left": 429.953125, "top": 389.4375 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0", "tool_shed_repository": { "changeset_revision": "7e801ab2b70e", "name": "fasta_to_tabular", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "614def54-f941-49a4-950c-69f651e6b35f", "workflow_outputs": [] }, "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", "id": 5, "input_connections": { "infile": { "id": 3, "output_name": "out_file1" } }, "inputs": [ { "description": "runtime parameter for tool Unique", "name": "infile" } ], "label": null, "name": "Unique", "outputs": [ { "name": "outfile", "type": "input" } ], "position": { "left": 659.984375, "top": 199.9375 }, "post_job_actions": { "HideDatasetActionoutfile": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "outfile" } }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0", "tool_shed_repository": { "changeset_revision": "20344ce0c811", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"false\\\"\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "1.1.0", "type": "tool", "uuid": "55da94d2-b1d9-46ed-9668-db9b7f19a5bb", "workflow_outputs": [] }, "6": { "annotation": "", "content_id": "Cut1", "id": 6, "input_connections": { "input": { "id": 4, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Cut", "name": "input" } ], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 675.953125, "top": 389.4375 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.2", "type": "tool", "uuid": "5bae54ed-b8c8-432c-9980-422d0f678be3", "workflow_outputs": [] }, "7": { "annotation": "", "content_id": "Cut1", "id": 7, "input_connections": { "input": { "id": 5, "output_name": "outfile" } }, "inputs": [ { "description": "runtime parameter for tool Cut", "name": "input" } ], "label": null, "name": "Cut", "outputs": [ { "name": "out_file1", "type": "tabular" } ], "position": { "left": 917.9375, "top": 198.46875 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "Cut1", "tool_state": "{\"columnList\": \"\\\"c1\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"delimiter\": \"\\\"U\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.2", "type": "tool", "uuid": "d6dc6ba2-efc0-4e90-8562-4739c4f41fab", "workflow_outputs": [] }, "8": { "annotation": "", "content_id": "comp1", "id": 8, "input_connections": { "input1": { "id": 6, "output_name": "out_file1" }, "input2": { "id": 7, "output_name": "out_file1" } }, "inputs": [ { "description": "runtime parameter for tool Compare two Datasets", "name": "input2" }, { "description": "runtime parameter for tool Compare two Datasets", "name": "input1" } ], "label": null, "name": "Compare two Datasets", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1123.9375, "top": 363.453125 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "comp1", "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"field2\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"field1\": \"\\\"1\\\"\", \"mode\": \"\\\"V\\\"\", \"chromInfo\": \"\\\"/tgac/services/galaxy/test/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.2", "type": "tool", "uuid": "7c71fbae-828d-4c99-8f7b-fe1a90b27626", "workflow_outputs": [] }, "9": { "annotation": "", "content_id": "cat1", "id": 9, "input_connections": { "input1": { "id": 8, "output_name": "out_file1" }, "queries_0|input2": { "id": 2, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Concatenate datasets", "name": "input1" } ], "label": null, "name": "Concatenate datasets", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 1130.5, "top": 686 }, "post_job_actions": { "HideDatasetActionout_file1": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "out_file1" } }, "tool_errors": null, "tool_id": "cat1", "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"queries\": \"[{\\\"input2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__index__\\\": 0}]\"}", "tool_version": "1.0.0", "type": "tool", "uuid": "8a1e29ca-8dec-4143-9db1-f38f820b0e9a", "workflow_outputs": [] }, "10": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", "id": 10, "input_connections": { "identifiers": { "id": 9, "output_name": "out_file1" }, "input": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool Filter by FASTA IDs", "name": "input" }, { "description": "runtime parameter for tool Filter by FASTA IDs", "name": "identifiers" } ], "label": null, "name": "Filter by FASTA IDs", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "left": 1392.921875, "top": 550.453125 }, "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", "tool_shed_repository": { "changeset_revision": "8d15aebf55fd", "name": "filter_by_fasta_ids", "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"identifiers\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dedup\": \"\\\"true\\\"\", \"__page__\": 0}", "tool_version": "1.0", "type": "tool", "uuid": "5f5fb6ac-f026-41bc-a89c-2d1d882ece85", "workflow_outputs": [ { "label": null, "output_name": "output", "uuid": "56824bb4-df6b-4ebc-8c89-c6731b5d76f1" } ] } }, "uuid": "cf6b9210-2ed8-46b1-920e-ac6303ed44d5" }