Mercurial > repos > earlhaminst > geneseqtofamily
diff GeneSeqToFamily.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 | 58c9294400ed |
line wrap: on
line diff
--- a/GeneSeqToFamily.ga Mon Jan 09 15:06:04 2017 -0500 +++ b/GeneSeqToFamily.ga Mon Feb 20 12:57:16 2017 -0500 @@ -12,19 +12,19 @@ "inputs": [ { "description": "", - "name": "CDS sequences" + "name": "CDS" } ], - "label": null, + "label": "CDS", "name": "Input dataset", "outputs": [], "position": { - "left": 620, - "top": 388.875 + "left": 350.0625, + "top": 418.0625 }, "tool_errors": null, "tool_id": null, - "tool_state": "{\"name\": \"CDS sequences\"}", + "tool_state": "{\"name\": \"CDS\"}", "tool_version": null, "type": "data_input", "uuid": "d2777a78-6429-47f6-9567-cb15140ace8d", @@ -44,19 +44,19 @@ "inputs": [ { "description": "", - "name": "Genes" + "name": "Gene feature information" } ], - "label": null, + "label": "Gene feature information", "name": "Input dataset", "outputs": [], "position": { - "left": 612.8125, - "top": 1110.9375 + "left": 342.875, + "top": 1140.125 }, "tool_errors": null, "tool_id": null, - "tool_state": "{\"name\": \"Genes\"}", + "tool_state": "{\"name\": \"Gene feature information\"}", "tool_version": null, "type": "data_input", "uuid": "3fbf4a09-9207-4a18-a133-0d865f9614f6", @@ -76,19 +76,19 @@ "inputs": [ { "description": "", - "name": "species tree" + "name": "Species tree" } ], - "label": null, + "label": "Species tree", "name": "Input dataset", "outputs": [], "position": { - "left": 605.9375, - "top": 1409 + "left": 336, + "top": 1438.171875 }, "tool_errors": null, "tool_id": null, - "tool_state": "{\"name\": \"species tree\"}", + "tool_state": "{\"name\": \"Species tree\"}", "tool_version": null, "type": "data_input", "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3", @@ -125,8 +125,8 @@ } ], "position": { - "left": 847.0625, - "top": 388.875 + "left": 577.125, + "top": 418.0625 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -178,8 +178,8 @@ } ], "position": { - "left": 1094.1875, - "top": 170.8125 + "left": 824.25, + "top": 199.984375 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -235,8 +235,8 @@ } ], "position": { - "left": 1351.4375, - "top": 398.9375 + "left": 1081.5, + "top": 428.125 }, "post_job_actions": { "HideDatasetActionoutput1": { @@ -284,16 +284,10 @@ } ], "position": { - "left": 1671.4375, - "top": 472.8125 + "left": 1401.5, + "top": 502 }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, + "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.1", "tool_shed_repository": { @@ -306,7 +300,13 @@ "tool_version": "0.1.1", "type": "tool", "uuid": "3eb98d54-a52d-4605-b068-28a700290d92", - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "6473f6a6-9036-43f2-ba10-961cecfb351f" + } + ] }, "7": { "annotation": "", @@ -337,8 +337,8 @@ } ], "position": { - "left": 1907.9375, - "top": 402.875 + "left": 1638, + "top": 432.0625 }, "post_job_actions": { "HideDatasetActionoutputFile": { @@ -363,59 +363,16 @@ }, "8": { "annotation": "", - "content_id": "Filter1", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", "id": 8, "input_connections": { - "input": { + "inputFile": { "id": 7, "output_name": "outputFile" } }, "inputs": [ { - "description": "runtime parameter for tool Filter", - "name": "input" - } - ], - "label": null, - "name": "Filter", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 2142, - "top": 199 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Filter1", - "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c2>2\\\"\", \"__page__\": 0}", - "tool_version": "1.1.0", - "type": "tool", - "uuid": "b2126c05-5d8d-4529-84fd-1b6f7f03a0ab", - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.1.1", - "id": 9, - "input_connections": { - "inputFile": { - "id": 8, - "output_name": "out_file1" - } - }, - "inputs": [ - { "description": "runtime parameter for tool hcluster_sg_parser", "name": "inputFile" } @@ -426,11 +383,15 @@ { "name": "ids_lists", "type": "input" + }, + { + "name": "discarded", + "type": "txt" } ], "position": { - "left": 2252.625, - "top": 441.8125 + "left": 1950.0625, + "top": 477.171875 }, "post_job_actions": { "HideDatasetActionids_lists": { @@ -440,26 +401,32 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.1.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", "tool_shed_repository": { - "changeset_revision": "dbc49bd1a3e9", + "changeset_revision": "17aa68582a05", "name": "hcluster_sg_parser", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "0.1.1", + "tool_state": "{\"__page__\": 0, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.2.0", "type": "tool", - "uuid": "3ad63783-ce49-4e1d-b502-3c594b0d4bd7", - "workflow_outputs": [] + "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60", + "workflow_outputs": [ + { + "label": null, + "output_name": "discarded", + "uuid": "465afc7e-afad-4228-bb28-2f7b1304a771" + } + ] }, - "10": { + "9": { "annotation": "", "content_id": "trimmer", - "id": 10, + "id": 9, "input_connections": { "input1": { - "id": 9, + "id": 8, "output_name": "ids_lists" } }, @@ -478,8 +445,8 @@ } ], "position": { - "left": 1032.6875, - "top": 1044 + "left": 826.75, + "top": 1053.171875 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -496,17 +463,17 @@ "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3", "workflow_outputs": [] }, - "11": { + "10": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8", - "id": 11, + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", + "id": 10, "input_connections": { "input_type|fasta_input": { "id": 3, "output_name": "out_file1" }, "input_type|identifiers": { - "id": 9, + "id": 8, "output_name": "ids_lists" } }, @@ -524,10 +491,6 @@ "name": "T-Coffee", "outputs": [ { - "name": "cigar", - "type": "tabular" - }, - { "name": "clustalw_aln", "type": "clustalw" }, @@ -569,15 +532,10 @@ } ], "position": { - "left": 1910.9375, - "top": 673.4375 + "left": 1641, + "top": 702.625 }, "post_job_actions": { - "HideDatasetActioncigar": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "cigar" - }, "HideDatasetActionclustalw_aln": { "action_arguments": {}, "action_type": "HideDatasetAction", @@ -630,26 +588,26 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8", + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", "tool_shed_repository": { - "changeset_revision": "b3833e5b50d4", + "changeset_revision": "78dd29aa7fc1", "name": "t_coffee", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"identifiers\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"fasta_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"cigar\\\", \\\"fasta_aln\\\"]\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", - "tool_version": "11.0.8", + "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"identifiers\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"fasta_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"fasta_aln\\\"]\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", + "tool_version": "11.0.8_1", "type": "tool", "uuid": "827ba178-5028-4ae4-b5e1-f234bcfce9f8", "workflow_outputs": [] }, - "12": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", - "id": 12, + "id": 11, "input_connections": { "identifiers": { - "id": 10, + "id": 9, "output_name": "out_file1" }, "input": { @@ -676,8 +634,8 @@ } ], "position": { - "left": 1336.8125, - "top": 1028.875 + "left": 1154.875, + "top": 980.0625 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -700,17 +658,17 @@ "uuid": "b22832ea-47b0-46a1-87da-e362672133b1", "workflow_outputs": [] }, - "13": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", - "id": 13, + "id": 12, "input_connections": { "input1": { - "id": 12, + "id": 11, "output_name": "output" }, "input2": { - "id": 11, + "id": 10, "output_name": "fasta_aln" } }, @@ -733,8 +691,8 @@ } ], "position": { - "left": 1643.875, - "top": 1215.875 + "left": 1373.9375, + "top": 1245.0625 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -757,13 +715,13 @@ "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", "workflow_outputs": [] }, - "14": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", - "id": 14, + "id": 13, "input_connections": { "aln": { - "id": 13, + "id": 12, "output_name": "out_file1" }, "species_tree": { @@ -794,8 +752,8 @@ } ], "position": { - "left": 1900.9375, - "top": 1414.375 + "left": 1631, + "top": 1443.5625 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -818,21 +776,21 @@ "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", "workflow_outputs": [] }, - "15": { + "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.1.0", - "id": 15, + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.2.0", + "id": 14, "input_connections": { "alignmentFile": { - "id": 11, - "output_name": "cigar" + "id": 10, + "output_name": "fasta_aln" }, "genesFile": { "id": 1, "output_name": "output" }, "treeFile": { - "id": 14, + "id": 13, "output_name": "output" } }, @@ -859,20 +817,20 @@ } ], "position": { - "left": 2507.9375, - "top": 1050.375 + "left": 2238, + "top": 1079.5625 }, "post_job_actions": {}, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.1.0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.2.0", "tool_shed_repository": { - "changeset_revision": "af9f72ddf7f9", + "changeset_revision": "fc8ca4ade638", "name": "gafa", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__page__\": 0, \"treeFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"alignmentFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"genesFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "0.1.0", + "tool_version": "0.2.0", "type": "tool", "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", "workflow_outputs": [ @@ -884,5 +842,5 @@ ] } }, - "uuid": "7ae94ea4-e34a-4e09-a15c-31839c6e5eef" + "uuid": "8a774cd5-046c-4272-badd-8e84aaed9c0f" }