Mercurial > repos > earlhaminst > geneseqtofamily
changeset 4:cc5419f7dff7 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit efb6a192c36d4e8aa6d24d692890025ffd8a0e65-dirty
author | earlhaminst |
---|---|
date | Mon, 27 Nov 2017 11:04:05 -0500 |
parents | fd620c523d63 |
children | 06470b2e491f |
files | GeneSeqToFamily.ga |
diffstat | 1 files changed, 119 insertions(+), 118 deletions(-) [+] |
line wrap: on
line diff
--- a/GeneSeqToFamily.ga Thu May 18 14:09:32 2017 -0400 +++ b/GeneSeqToFamily.ga Mon Nov 27 11:04:05 2017 -0500 @@ -7,6 +7,7 @@ "0": { "annotation": "", "content_id": null, + "errors": null, "id": 0, "input_connections": {}, "inputs": [ @@ -19,10 +20,9 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 239.066650390625, - "top": 418.06666564941406 + "left": 200, + "top": 266 }, - "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"CDS\"}", "tool_version": null, @@ -39,6 +39,7 @@ "1": { "annotation": "", "content_id": null, + "errors": null, "id": 1, "input_connections": {}, "inputs": [ @@ -51,10 +52,9 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 231.88333129882812, - "top": 1140.13330078125 + "left": 202.8125, + "top": 469.0625 }, - "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Gene feature information\"}", "tool_version": null, @@ -71,6 +71,7 @@ "2": { "annotation": "", "content_id": null, + "errors": null, "id": 2, "input_connections": {}, "inputs": [ @@ -83,10 +84,9 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 229, - "top": 1438.1666870117188 + "left": 201.921875, + "top": 903.09375 }, - "tool_errors": null, "tool_id": null, "tool_state": "{\"name\": \"Species tree\"}", "tool_version": null, @@ -103,6 +103,7 @@ "3": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", + "errors": null, "id": 3, "input_connections": { "input1": { @@ -125,8 +126,8 @@ } ], "position": { - "left": 607.1333312988281, - "top": 432.06666564941406 + "left": 460.0625, + "top": 200 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -135,7 +136,6 @@ "output_name": "out_file1" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", "tool_shed_repository": { "changeset_revision": "1b6538ec8b56", @@ -143,7 +143,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"0\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"trim\": \"\\\"no\\\"\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"frame\": \"\\\"1\\\"\", \"regions\": \"\\\"\\\"\", \"clean\": \"\\\"no\\\"\", \"table\": \"\\\"0\\\"\", \"alternative\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "5.0.0", "type": "tool", "uuid": "12722a4e-291d-4ba2-b7f8-77209049b0ac", @@ -152,6 +152,7 @@ "4": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", + "errors": null, "id": 4, "input_connections": { "input_file": { @@ -178,8 +179,8 @@ } ], "position": { - "left": 727.25, - "top": 196.98333740234375 + "left": 644.171875, + "top": 294.890625 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -188,16 +189,15 @@ "output_name": "outfile" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", "tool_shed_repository": { - "changeset_revision": "3034ce97dd33", + "changeset_revision": "6f386c5dc4fb", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"title\": \"\\\"\\\"\", \"dbtype\": \"\\\"prot\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"parse_seqids\": \"\\\"false\\\"\"}", - "tool_version": "0.1.08", + "tool_state": "{\"__page__\": null, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dbtype\": \"\\\"prot\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}", + "tool_version": "0.2.01", "type": "tool", "uuid": "c72477fb-cc1d-45ec-a0cd-8215be8fe8ee", "workflow_outputs": [] @@ -205,6 +205,7 @@ "5": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", + "errors": null, "id": 5, "input_connections": { "db_opts|histdb": { @@ -235,8 +236,8 @@ } ], "position": { - "left": 970.5, - "top": 428.1333312988281 + "left": 929.421875, + "top": 205.0625 }, "post_job_actions": { "HideDatasetActionoutput1": { @@ -245,16 +246,15 @@ "output_name": "output1" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.08", "tool_shed_repository": { - "changeset_revision": "3034ce97dd33", + "changeset_revision": "6f386c5dc4fb", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"evalue_cutoff\": \"\\\"1e-10\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"matrix\\\": \\\"BLOSUM62\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"filter_query\\\": \\\"false\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"90.0\\\", \\\"max_hits\\\": \\\"3\\\"}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastp\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"ext\\\", \\\"__current_case__\\\": 1}\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "0.1.08", + "tool_state": "{\"evalue_cutoff\": \"\\\"1e-10\\\"\", \"__page__\": null, \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"use_sw_tback\\\": \\\"false\\\", \\\"matrix\\\": \\\"BLOSUM62\\\", \\\"max_hsps\\\": \\\"1\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"filter_query\\\": \\\"false\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"max_hits\\\": \\\"0\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast_type\": \"\\\"blastp\\\"\", \"output\": \"{\\\"out_format\\\": \\\"ext\\\", \\\"__current_case__\\\": 1}\"}", + "tool_version": "0.2.01", "type": "tool", "uuid": "7ee928f5-88bf-4d8d-9b0a-072560a9e410", "workflow_outputs": [] @@ -262,6 +262,7 @@ "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.1", + "errors": null, "id": 6, "input_connections": { "input": { @@ -284,20 +285,19 @@ } ], "position": { - "left": 1290.5, - "top": 502 + "left": 1134.421875, + "top": 380.921875 }, "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": { - "changeset_revision": "fd11653657f9", + "changeset_revision": "363f3480622d", "name": "blast_parser", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "0.1.1", + "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reciprocal\": \"\\\"true\\\"\", \"__page__\": null}", + "tool_version": "0.1.2", "type": "tool", "uuid": "3eb98d54-a52d-4605-b068-28a700290d92", "workflow_outputs": [ @@ -311,6 +311,7 @@ "7": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1", + "errors": null, "id": 7, "input_connections": { "inputFile": { @@ -321,7 +322,7 @@ "inputs": [ { "description": "runtime parameter for tool hcluster_sg", - "name": "C" + "name": "c_conditional" }, { "description": "runtime parameter for tool hcluster_sg", @@ -337,8 +338,8 @@ } ], "position": { - "left": 1527, - "top": 432.06666564941406 + "left": 1317.921875, + "top": 207 }, "post_job_actions": { "HideDatasetActionoutputFile": { @@ -347,16 +348,15 @@ "output_name": "outputFile" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1", "tool_shed_repository": { - "changeset_revision": "09955cea320f", + "changeset_revision": "1d2de27d7a9c", "name": "hcluster_sg", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"c\": \"\\\"true\\\"\", \"b\": \"\\\"0.1\\\"\", \"__rerun_remap_job_id__\": null, \"m\": \"\\\"500\\\"\", \"C\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"O\": \"{\\\"O_selector\\\": \\\"\\\", \\\"__current_case__\\\": 1}\", \"L\": \"\\\"2\\\"\", \"s\": \"\\\"0.5\\\"\", \"w\": \"\\\"20\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", - "tool_version": "0.5.1", + "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"c_conditional\": \"{\\\"c\\\": \\\"\\\", \\\"b\\\": \\\"0.1\\\", \\\"m\\\": \\\"500\\\", \\\"C\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"O\\\": {\\\"O_selector\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"L\\\": \\\"2\\\", \\\"s\\\": \\\"0.34\\\", \\\"__current_case__\\\": 1}\", \"w\": \"\\\"0\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "0.5.1.1", "type": "tool", "uuid": "d2b2ba89-b47d-4241-8adf-0d780f834412", "workflow_outputs": [] @@ -364,6 +364,7 @@ "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", + "errors": null, "id": 8, "input_connections": { "inputFile": { @@ -373,12 +374,12 @@ }, "inputs": [ { - "description": "runtime parameter for tool hcluster_sg_parser", + "description": "runtime parameter for tool hcluster_sg parser", "name": "inputFile" } ], "label": null, - "name": "hcluster_sg_parser", + "name": "hcluster_sg parser", "outputs": [ { "name": "ids_lists", @@ -390,8 +391,8 @@ } ], "position": { - "left": 1839.066650390625, - "top": 477.1666717529297 + "left": 1298, + "top": 505.09375 }, "post_job_actions": { "HideDatasetActionids_lists": { @@ -400,15 +401,14 @@ "output_name": "ids_lists" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", "tool_shed_repository": { - "changeset_revision": "17aa68582a05", + "changeset_revision": "f9e418125021", "name": "hcluster_sg_parser", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__page__\": 0, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_state": "{\"__page__\": null, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "0.2.0", "type": "tool", "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60", @@ -422,52 +422,10 @@ }, "9": { "annotation": "", - "content_id": "trimmer", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", + "errors": null, "id": 9, "input_connections": { - "input1": { - "id": 8, - "output_name": "ids_lists" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Trim", - "name": "input1" - } - ], - "label": null, - "name": "Trim", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 715.75, - "top": 1053.1666870117188 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "trimmer", - "tool_state": "{\"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"end\": \"\\\"-2\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"null\", \"start\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"col\": \"\\\"0\\\"\"}", - "tool_version": "0.0.1", - "type": "tool", - "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3", - "workflow_outputs": [] - }, - "10": { - "annotation": "", - "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" @@ -532,8 +490,8 @@ } ], "position": { - "left": 1530, - "top": 702.6333312988281 + "left": 713.921875, + "top": 521.5625 }, "post_job_actions": { "HideDatasetActionclustalw_aln": { @@ -587,27 +545,70 @@ "output_name": "score_html" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", "tool_shed_repository": { - "changeset_revision": "fa59d6fea7f5", + "changeset_revision": "a91be6005274", "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\": \"[\\\"fasta_aln\\\"]\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", + "tool_state": "{\"__page__\": null, \"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": [] }, + "10": { + "annotation": "", + "content_id": "trimmer", + "errors": null, + "id": 10, + "input_connections": { + "input1": { + "id": 8, + "output_name": "ids_lists" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Trim", + "name": "input1" + } + ], + "label": null, + "name": "Trim", + "outputs": [ + { + "name": "out_file1", + "type": "input" + } + ], + "position": { + "left": 449.671875, + "top": 777.09375 + }, + "post_job_actions": { + "HideDatasetActionout_file1": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "trimmer", + "tool_state": "{\"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"end\": \"\\\"-2\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"null\", \"start\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"col\": \"\\\"0\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3", + "workflow_outputs": [] + }, "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0", + "errors": null, "id": 11, "input_connections": { "identifiers": { - "id": 9, + "id": 10, "output_name": "out_file1" }, "input": { @@ -634,8 +635,8 @@ } ], "position": { - "left": 1043.8833312988281, - "top": 980.066650390625 + "left": 575.8125, + "top": 980 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -644,7 +645,6 @@ "output_name": "output" } }, - "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", @@ -652,7 +652,7 @@ "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_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"identifiers\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dedup\": \"\\\"true\\\"\", \"__page__\": null}", "tool_version": "1.0", "type": "tool", "uuid": "b22832ea-47b0-46a1-87da-e362672133b1", @@ -661,6 +661,7 @@ "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", + "errors": null, "id": 12, "input_connections": { "input1": { @@ -668,7 +669,7 @@ "output_name": "output" }, "input2": { - "id": 10, + "id": 9, "output_name": "fasta_aln" } }, @@ -691,8 +692,8 @@ } ], "position": { - "left": 1239.933349609375, - "top": 1227.066650390625 + "left": 952.84375, + "top": 879 }, "post_job_actions": { "HideDatasetActionout_file1": { @@ -701,7 +702,6 @@ "output_name": "out_file1" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", "tool_shed_repository": { "changeset_revision": "1b6538ec8b56", @@ -709,7 +709,7 @@ "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"__rerun_remap_job_id__\": null, \"table\": \"\\\"0\\\"\"}", + "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"__rerun_remap_job_id__\": null, \"table\": \"\\\"0\\\"\"}", "tool_version": "5.0.0", "type": "tool", "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", @@ -718,6 +718,7 @@ "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", + "errors": null, "id": 13, "input_connections": { "aln": { @@ -732,11 +733,11 @@ "inputs": [ { "description": "runtime parameter for tool TreeBeST best", - "name": "C" + "name": "aln" }, { "description": "runtime parameter for tool TreeBeST best", - "name": "aln" + "name": "C" }, { "description": "runtime parameter for tool TreeBeST best", @@ -752,8 +753,8 @@ } ], "position": { - "left": 1520, - "top": 1443.566650390625 + "left": 1173.921875, + "top": 967.5 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -762,7 +763,6 @@ "output_name": "output" } }, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2", "tool_shed_repository": { "changeset_revision": "66170848da6c", @@ -770,7 +770,7 @@ "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"A\": \"\\\"false\\\"\", \"a\": \"{\\\"a_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}\", \"C\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"b\": \"\\\"0.01\\\"\", \"d\": \"\\\"0.15\\\"\", \"aln\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"F\": \"\\\"11\\\"\", \"__page__\": 0, \"s\": \"\\\"false\\\"\", \"k\": \"{\\\"__current_case__\\\": 0, \\\"k_selector\\\": \\\"yes\\\"}\", \"c\": \"\\\"2\\\"\", \"L\": \"\\\"0.2\\\"\", \"P\": \"\\\"false\\\"\", \"S\": \"\\\"false\\\"\", \"r\": \"\\\"false\\\"\", \"g\": \"\\\"false\\\"\", \"species_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"N\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"l\": \"\\\"0.1\\\"\"}", + "tool_state": "{\"A\": \"\\\"false\\\"\", \"aln\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"C\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"b\": \"\\\"0.01\\\"\", \"d\": \"\\\"0.15\\\"\", \"g\": \"\\\"false\\\"\", \"F\": \"\\\"11\\\"\", \"S\": \"\\\"false\\\"\", \"__page__\": null, \"k\": \"{\\\"__current_case__\\\": 0, \\\"k_selector\\\": \\\"yes\\\"}\", \"c\": \"\\\"2\\\"\", \"L\": \"\\\"0.2\\\"\", \"P\": \"\\\"false\\\"\", \"s\": \"\\\"false\\\"\", \"r\": \"\\\"false\\\"\", \"a\": \"{\\\"a_selector\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}\", \"species_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"N\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"l\": \"\\\"0.1\\\"\"}", "tool_version": "1.9.2", "type": "tool", "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", @@ -779,10 +779,11 @@ "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", + "errors": null, "id": 14, "input_connections": { "alignmentFile": { - "id": 10, + "id": 9, "output_name": "fasta_aln" }, "genesFile": { @@ -817,19 +818,18 @@ } ], "position": { - "left": 2106, - "top": 1062.566650390625 + "left": 1299.921875, + "top": 747.5 }, "post_job_actions": {}, - "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", "tool_shed_repository": { - "changeset_revision": "117fc7414307", + "changeset_revision": "c388666f58e0", "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_state": "{\"__page__\": null, \"treeFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"alignmentFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"genesFile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "tool_version": "0.3.0", "type": "tool", "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", @@ -842,5 +842,6 @@ ] } }, - "uuid": "c4ee74fc-2f82-4be2-83f0-b687365d7524" -} + "tags": [], + "uuid": "bbf45200-b853-41bf-a853-abb1dec8ca9d" +} \ No newline at end of file