Mercurial > repos > earlhaminst > geneseqtofamily
diff GeneSeqToFamily.ga @ 7:e732a731f778 draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/workflows/GeneSeqToFamily commit 15c020a20c5dbf2fcb1cd9bb3865e9e936981f3c
| author | earlhaminst |
|---|---|
| date | Thu, 01 Sep 2022 11:32:32 +0000 |
| parents | 266800d51605 |
| children |
line wrap: on
line diff
--- a/GeneSeqToFamily.ga Thu Jun 10 16:18:59 2021 +0000 +++ b/GeneSeqToFamily.ga Thu Sep 01 11:32:32 2022 +0000 @@ -1,954 +1,1126 @@ { - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "GeneSeqToFamily", + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "GeneSeqToFamily", "steps": { "0": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 0, - "input_connections": {}, + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, "inputs": [ { - "description": "", + "description": "", "name": "CDS" } - ], - "label": "CDS", - "name": "Input dataset", - "outputs": [], + ], + "label": "CDS", + "name": "Input dataset", + "outputs": [], "position": { - "left": 225.984375, - "top": 532.5 - }, - "tool_id": null, - "tool_state": "{\"name\": \"CDS\"}", - "tool_version": null, - "type": "data_input", - "uuid": "d2777a78-6429-47f6-9567-cb15140ace8d", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "7eedd485-b41e-4b55-9359-9f7e56d84f54" - } - ] - }, + "bottom": 4.8000030517578125, + "height": 61.80000305175781, + "left": 178.98333740234375, + "right": 378.98333740234375, + "top": -57, + "width": 200, + "x": 178.98333740234375, + "y": -57 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "d2777a78-6429-47f6-9567-cb15140ace8d", + "workflow_outputs": [] + }, "1": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, + "annotation": "", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, "inputs": [ { - "description": "", + "description": "", "name": "Species tree" } - ], - "label": "Species tree", - "name": "Input dataset", - "outputs": [], + ], + "label": "Species tree", + "name": "Input dataset", + "outputs": [], "position": { - "left": 244.875, - "top": 947.578125 - }, - "tool_id": null, - "tool_state": "{\"name\": \"Species tree\"}", - "tool_version": null, - "type": "data_input", - "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "50734600-41fa-437a-9b2b-6572fd8763a2" - } - ] - }, + "bottom": 419.88331604003906, + "height": 61.80000305175781, + "left": 197.88333129882812, + "right": 397.8833312988281, + "top": 358.08331298828125, + "width": 200, + "x": 197.88333129882812, + "y": 358.08331298828125 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "1f2ca308-faad-44fa-ba48-fff5aeecbbd3", + "workflow_outputs": [] + }, "2": { - "annotation": "", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, + "annotation": "", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, "inputs": [ { - "description": "", + "description": "", "name": "Gene feature information" } - ], - "label": "Gene feature information", - "name": "Input dataset", - "outputs": [], + ], + "label": "Gene feature information", + "name": "Input dataset", + "outputs": [], "position": { - "left": 247.796875, - "top": 1200.5625 - }, - "tool_id": null, - "tool_state": "{\"name\": \"Gene feature information\"}", - "tool_version": null, - "type": "data_input", - "uuid": "3fbf4a09-9207-4a18-a133-0d865f9614f6", - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "39787c6d-ecd8-4147-b718-83d739202b3b" - } - ] - }, + "bottom": 693.2666473388672, + "height": 82.19999694824219, + "left": 200.8000030517578, + "right": 400.8000030517578, + "top": 611.066650390625, + "width": 200, + "x": 200.8000030517578, + "y": 611.066650390625 + }, + "tool_id": null, + "tool_state": "{\"optional\": false}", + "tool_version": null, + "type": "data_input", + "uuid": "3fbf4a09-9207-4a18-a133-0d865f9614f6", + "workflow_outputs": [] + }, "3": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", - "errors": null, - "id": 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": { - "id": 0, + "id": 0, "output_name": "output" } - }, - "inputs": [], - "label": null, - "name": "transeq", + }, + "inputs": [], + "label": null, + "name": "transeq", "outputs": [ { - "name": "out_file1", + "name": "out_file1", "type": "fasta" } - ], + ], "position": { - "left": 550.046875, - "top": 260.484375 - }, + "bottom": -235.81666564941406, + "height": 93.19999694824219, + "left": 503.04998779296875, + "right": 703.0499877929688, + "top": -329.01666259765625, + "width": 200, + "x": 503.04998779296875, + "y": -329.01666259765625 + }, "post_job_actions": { "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "out_file1" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0", "tool_shed_repository": { - "changeset_revision": "dc492eb6a4fc", - "name": "emboss_5", - "owner": "devteam", + "changeset_revision": "dc492eb6a4fc", + "name": "emboss_5", + "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"trim\": \"\\\"yes\\\"\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"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", + }, + "tool_state": "{\"alternative\": \"no\", \"clean\": \"no\", \"frame\": \"1\", \"input1\": {\"__class__\": \"ConnectedValue\"}, \"out_format1\": \"fasta\", \"regions\": \"\", \"table\": \"0\", \"trim\": \"yes\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.0.0", + "type": "tool", + "uuid": "12722a4e-291d-4ba2-b7f8-77209049b0ac", "workflow_outputs": [] - }, + }, "4": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", - "errors": null, - "id": 4, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", + "errors": null, + "id": 4, "input_connections": { "input": { - "id": 3, + "id": 3, "output_name": "out_file1" } - }, - "inputs": [], - "label": null, - "name": "Filter FASTA", + }, + "inputs": [], + "label": null, + "name": "Filter FASTA", "outputs": [ { - "name": "output", + "name": "output", "type": "fasta" - }, + }, { - "name": "discarded", + "name": "discarded", "type": "fasta" } - ], + ], "position": { - "left": 552.484375, - "top": 427.984375 - }, + "bottom": 43.68333435058594, + "height": 205.1999969482422, + "left": 505.48333740234375, + "right": 705.4833374023438, + "top": -161.51666259765625, + "width": 200, + "x": 505.48333740234375, + "y": -161.51666259765625 + }, "post_job_actions": { "HideDatasetActiondiscarded": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "discarded" - }, + }, "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", + "tool_shed_repository": { + "changeset_revision": "cd22452edec2", + "name": "filter_by_fasta_ids", + "owner": "galaxyp", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"dedup\": \"true\", \"header_criteria\": {\"header_criteria_select\": \"\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_discarded\": \"true\", \"sequence_criteria\": {\"sequence_criteria_select\": \"regexp\", \"__current_case__\": 2, \"regexp\": \"^[^*]+$\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2", + "type": "tool", + "uuid": "8dd011eb-b442-42cf-b528-331739f3d252", + "workflow_outputs": [] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0", + "errors": null, + "id": 5, + "input_connections": { + "input_file": { + "id": 4, "output_name": "output" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", + }, + "inputs": [ + { + "description": "runtime parameter for tool NCBI BLAST+ makeblastdb", + "name": "mask_data_file" + } + ], + "label": null, + "name": "NCBI BLAST+ makeblastdb", + "outputs": [ + { + "name": "outfile", + "type": "data" + } + ], + "position": { + "bottom": 113.66667175292969, + "height": 184.8000030517578, + "left": 785.13330078125, + "right": 985.13330078125, + "top": -71.13333129882812, + "width": 200, + "x": 785.13330078125, + "y": -71.13333129882812 + }, + "post_job_actions": { + "HideDatasetActionoutfile": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0", "tool_shed_repository": { - "changeset_revision": "cd22452edec2", - "name": "filter_by_fasta_ids", - "owner": "galaxyp", + "changeset_revision": "c877294f8025", + "name": "ncbi_blast_plus", + "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dedup\": \"\\\"true\\\"\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"header_criteria\": \"{\\\"__current_case__\\\": 0, \\\"header_criteria_select\\\": \\\"\\\"}\", \"output_discarded\": \"\\\"true\\\"\", \"sequence_criteria\": \"{\\\"__current_case__\\\": 2, \\\"regexp\\\": \\\"^[^*]+$\\\", \\\"sequence_criteria_select\\\": \\\"regexp\\\"}\"}", - "tool_version": "2.2", - "type": "tool", - "uuid": "8dd011eb-b442-42cf-b528-331739f3d252", + }, + "tool_state": "{\"dbtype\": \"prot\", \"hash_index\": \"true\", \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"mask_data_file\": {\"__class__\": \"RuntimeValue\"}, \"parse_seqids\": \"false\", \"tax\": {\"taxselect\": \"\", \"__current_case__\": 0}, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.3.0", + "type": "tool", + "uuid": "c72477fb-cc1d-45ec-a0cd-8215be8fe8ee", "workflow_outputs": [] - }, - "5": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332", - "errors": null, - "id": 5, + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332", + "errors": null, + "id": 6, "input_connections": { "input": { - "id": 4, + "id": 4, "output_name": "output" } - }, + }, "inputs": [ { - "description": "runtime parameter for tool faSplit", + "description": "runtime parameter for tool faSplit", "name": "O" } - ], - "label": null, - "name": "faSplit", + ], + "label": null, + "name": "faSplit", "outputs": [ { - "name": "output_list", + "name": "output_list", "type": "input" } - ], + ], "position": { - "left": 845.96875, - "top": 315 - }, + "bottom": -160.89999389648438, + "height": 113.60000610351562, + "left": 798.9666748046875, + "right": 998.9666748046875, + "top": -274.5, + "width": 200, + "x": 798.9666748046875, + "y": -274.5 + }, "post_job_actions": { "HideDatasetActionoutput_list": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "output_list" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332", "tool_shed_repository": { - "changeset_revision": "dc36d50254d8", - "name": "ucsc_fasplit", - "owner": "iuc", + "changeset_revision": "dc36d50254d8", + "name": "ucsc_fasplit", + "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"O\": \"{\\\"__current_case__\\\": 0, \\\"count\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"split_type\\\": \\\"sequence\\\"}\", \"__page__\": null}", - "tool_version": "332", - "type": "tool", - "uuid": "3f991f5d-a175-4df4-9870-0ff701437991", + }, + "tool_state": "{\"O\": {\"split_type\": \"sequence\", \"__current_case__\": 0, \"count\": {\"__class__\": \"RuntimeValue\"}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "332", + "type": "tool", + "uuid": "3f991f5d-a175-4df4-9870-0ff701437991", "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0", - "errors": null, - "id": 6, + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0", + "errors": null, + "id": 7, "input_connections": { - "input_file": { - "id": 4, - "output_name": "output" + "db_opts|histdb": { + "id": 5, + "output_name": "outfile" + }, + "query": { + "id": 6, + "output_name": "output_list" } - }, - "inputs": [ - { - "description": "runtime parameter for tool NCBI BLAST+ makeblastdb", - "name": "mask_data_file" - } - ], - "label": null, - "name": "NCBI BLAST+ makeblastdb", + }, + "inputs": [], + "label": null, + "name": "NCBI BLAST+ blastp", "outputs": [ { - "name": "outfile", - "type": "data" - } - ], - "position": { - "left": 832.140625, - "top": 518.359375 - }, - "post_job_actions": { - "HideDatasetActionoutfile": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0", - "tool_shed_repository": { - "changeset_revision": "c877294f8025", - "name": "ncbi_blast_plus", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"dbtype\": \"\\\"prot\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"title\": \"\\\"\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}", - "tool_version": "0.3.0", - "type": "tool", - "uuid": "c72477fb-cc1d-45ec-a0cd-8215be8fe8ee", - "workflow_outputs": [] - }, - "7": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0", - "errors": null, - "id": 7, - "input_connections": { - "db_opts|histdb": { - "id": 6, - "output_name": "outfile" - }, - "query": { - "id": 5, - "output_name": "output_list" - } - }, - "inputs": [], - "label": null, - "name": "NCBI BLAST+ blastp", - "outputs": [ - { - "name": "output1", + "name": "output1", "type": "tabular" } - ], + ], "position": { - "left": 1176.484375, - "top": 228 - }, + "bottom": -197.10000610351562, + "height": 164.39999389648438, + "left": 1129.4833984375, + "right": 1329.4833984375, + "top": -361.5, + "width": 200, + "x": 1129.4833984375, + "y": -361.5 + }, "post_job_actions": { "HideDatasetActionoutput1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0", + "tool_shed_repository": { + "changeset_revision": "c877294f8025", + "name": "ncbi_blast_plus", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"adv_opts\": {\"adv_opts_selector\": \"advanced\", \"__current_case__\": 1, \"filter_query\": \"false\", \"matrix_gapcosts\": {\"matrix\": \"\", \"__current_case__\": 0}, \"max_hits\": \"0\", \"max_hsps\": \"1\", \"word_size\": null, \"window_size\": null, \"threshold\": null, \"comp_based_stats\": \"\", \"parse_deflines\": \"false\", \"adv_optional_id_files_opts\": {\"adv_optional_id_files_opts_selector\": \"none\", \"__current_case__\": 0}, \"qcov_hsp_perc\": \"50.0\", \"use_sw_tback\": \"false\"}, \"blast_type\": \"blastp\", \"db_opts\": {\"db_opts_selector\": \"histdb\", \"__current_case__\": 1, \"database\": \"\", \"histdb\": {\"__class__\": \"ConnectedValue\"}, \"subject\": \"\"}, \"evalue_cutoff\": \"1e-10\", \"output\": {\"out_format\": \"ext\", \"__current_case__\": 1}, \"query\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.3.0", + "type": "tool", + "uuid": "b67576ce-b912-4b00-8277-0e422399f70c", + "workflow_outputs": [] + }, + "8": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0", + "errors": null, + "id": 8, + "input_connections": { + "inputs": { + "id": 7, "output_name": "output1" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0", - "tool_shed_repository": { - "changeset_revision": "c877294f8025", - "name": "ncbi_blast_plus", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"evalue_cutoff\": \"\\\"1e-10\\\"\", \"output\": \"{\\\"__current_case__\\\": 1, \\\"out_format\\\": \\\"ext\\\"}\", \"adv_opts\": \"{\\\"__current_case__\\\": 1, \\\"adv_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"comp_based_stats\\\": \\\"\\\", \\\"filter_query\\\": \\\"false\\\", \\\"matrix_gapcosts\\\": {\\\"__current_case__\\\": 0, \\\"matrix\\\": \\\"\\\"}, \\\"max_hits\\\": \\\"0\\\", \\\"max_hsps\\\": \\\"1\\\", \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"50.0\\\", \\\"threshold\\\": \\\"\\\", \\\"use_sw_tback\\\": \\\"false\\\", \\\"window_size\\\": \\\"\\\", \\\"word_size\\\": \\\"\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\", \\\"db_opts_selector\\\": \\\"histdb\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"subject\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastp\\\"\", \"query\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", - "tool_version": "0.3.0", - "type": "tool", - "uuid": "b67576ce-b912-4b00-8277-0e422399f70c", - "workflow_outputs": [] - }, - "8": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0", - "errors": null, - "id": 8, - "input_connections": { - "inputs": { - "id": 7, - "output_name": "output1" - } - }, - "inputs": [], - "label": null, - "name": "Concatenate datasets", + }, + "inputs": [], + "label": null, + "name": "Concatenate datasets", "outputs": [ { - "name": "out_file1", + "name": "out_file1", "type": "input" } - ], + ], "position": { - "left": 1214.484375, - "top": 439.984375 - }, + "bottom": -35.91667175292969, + "height": 113.59999084472656, + "left": 1167.4833984375, + "right": 1367.4833984375, + "top": -149.51666259765625, + "width": 200, + "x": 1167.4833984375, + "y": -149.51666259765625 + }, "post_job_actions": { "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "out_file1" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0", + "tool_shed_repository": { + "changeset_revision": "0a8c6b61f0f4", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"inputs\": {\"__class__\": \"ConnectedValue\"}, \"queries\": [], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.0", + "type": "tool", + "uuid": "8c9b7c9a-b37d-46c2-8004-e5cbd302c048", + "workflow_outputs": [] + }, + "9": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2", + "errors": null, + "id": 9, + "input_connections": { + "input": { + "id": 8, "output_name": "out_file1" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0", - "tool_shed_repository": { - "changeset_revision": "0a8c6b61f0f4", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"inputs\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"queries\": \"[]\"}", - "tool_version": "0.1.0", - "type": "tool", - "uuid": "8c9b7c9a-b37d-46c2-8004-e5cbd302c048", - "workflow_outputs": [] - }, - "9": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2", - "errors": null, - "id": 9, - "input_connections": { - "input": { - "id": 8, - "output_name": "out_file1" - } - }, - "inputs": [], - "label": null, - "name": "BLAST parser", + }, + "inputs": [], + "label": null, + "name": "BLAST parser", "outputs": [ { - "name": "output", + "name": "output", "type": "tabular" } - ], + ], "position": { - "left": 1266.390625, - "top": 587.390625 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2", + "bottom": 111.48333740234375, + "height": 113.60000610351562, + "left": 1219.38330078125, + "right": 1419.38330078125, + "top": -2.116668701171875, + "width": 200, + "x": 1219.38330078125, + "y": -2.116668701171875 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2", "tool_shed_repository": { - "changeset_revision": "363f3480622d", - "name": "blast_parser", - "owner": "earlhaminst", + "changeset_revision": "363f3480622d", + "name": "blast_parser", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"reciprocal\": \"\\\"true\\\"\", \"__page__\": null}", - "tool_version": "0.1.2", - "type": "tool", - "uuid": "3eb98d54-a52d-4605-b068-28a700290d92", + }, + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"reciprocal\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.1.2", + "type": "tool", + "uuid": "3eb98d54-a52d-4605-b068-28a700290d92", "workflow_outputs": [ { - "label": null, - "output_name": "output", - "uuid": "ecb78ea1-f143-4b34-96e3-ec4e885c17f2" + "label": null, + "output_name": "output", + "uuid": "45ce5eb3-b067-4374-a4e0-bde22241d0d9" } ] - }, + }, "10": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1", - "errors": null, - "id": 10, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1", + "errors": null, + "id": 10, "input_connections": { "inputFile": { - "id": 9, + "id": 9, "output_name": "output" } - }, + }, "inputs": [ { - "description": "runtime parameter for tool hcluster_sg", + "description": "runtime parameter for tool hcluster_sg", "name": "c_conditional" } - ], - "label": null, - "name": "hcluster_sg", + ], + "label": null, + "name": "hcluster_sg", "outputs": [ { - "name": "outputFile", + "name": "outputFile", "type": "tabular" } - ], + ], "position": { - "left": 1544.875, - "top": 392.484375 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1", + "bottom": -53.01666259765625, + "height": 144, + "left": 1497.88330078125, + "right": 1697.88330078125, + "top": -197.01666259765625, + "width": 200, + "x": 1497.88330078125, + "y": -197.01666259765625 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1", "tool_shed_repository": { - "changeset_revision": "1d2de27d7a9c", - "name": "hcluster_sg", - "owner": "earlhaminst", + "changeset_revision": "1d2de27d7a9c", + "name": "hcluster_sg", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"c_conditional\": \"{\\\"C\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"L\\\": \\\"2\\\", \\\"O\\\": {\\\"O_selector\\\": \\\"\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"b\\\": \\\"0.1\\\", \\\"c\\\": \\\"\\\", \\\"m\\\": \\\"500\\\", \\\"s\\\": \\\"0.34\\\"}\", \"w\": \"\\\"0\\\"\", \"inputFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", - "tool_version": "0.5.1.1", - "type": "tool", - "uuid": "d2b2ba89-b47d-4241-8adf-0d780f834412", + }, + "tool_state": "{\"c_conditional\": {\"c\": \"\", \"__current_case__\": 1, \"s\": \"0.34\", \"m\": \"500\", \"b\": \"0.1\", \"O\": {\"O_selector\": \"\", \"__current_case__\": 1}, \"C\": {\"__class__\": \"RuntimeValue\"}, \"L\": \"2\"}, \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"w\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.5.1.1", + "type": "tool", + "uuid": "d2b2ba89-b47d-4241-8adf-0d780f834412", "workflow_outputs": [ { - "label": null, - "output_name": "outputFile", - "uuid": "82fefa51-b192-49b2-bf41-e9914f179984" + "label": null, + "output_name": "outputFile", + "uuid": "f62dd72a-654e-48e3-b8f0-7d32c88ee0c9" } ] - }, + }, "11": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", - "errors": null, - "id": 11, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", + "errors": null, + "id": 11, "input_connections": { "inputFile": { - "id": 10, + "id": 10, "output_name": "outputFile" } - }, - "inputs": [], - "label": null, - "name": "hcluster_sg parser", + }, + "inputs": [], + "label": null, + "name": "hcluster_sg parser", "outputs": [ { - "name": "ids_lists", + "name": "ids_lists", "type": "input" - }, + }, { - "name": "discarded", + "name": "discarded", "type": "txt" } - ], + ], "position": { - "left": 1548.984375, - "top": 597.578125 - }, + "bottom": 213.28334045410156, + "height": 205.20001220703125, + "left": 1501.9833984375, + "right": 1701.9833984375, + "top": 8.083328247070312, + "width": 200, + "x": 1501.9833984375, + "y": 8.083328247070312 + }, "post_job_actions": { "HideDatasetActionids_lists": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "ids_lists" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0", "tool_shed_repository": { - "changeset_revision": "f9e418125021", - "name": "hcluster_sg_parser", - "owner": "earlhaminst", + "changeset_revision": "f9e418125021", + "name": "hcluster_sg_parser", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"max_elems\": \"\\\"200\\\"\", \"min_elems\": \"\\\"3\\\"\", \"__rerun_remap_job_id__\": null, \"inputFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", - "tool_version": "0.2.0", - "type": "tool", - "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60", + }, + "tool_state": "{\"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"max_elems\": \"200\", \"min_elems\": \"3\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.2.0", + "type": "tool", + "uuid": "df3ae47f-f5a3-4f44-9b25-9bc36b049d60", "workflow_outputs": [ { - "label": null, - "output_name": "discarded", - "uuid": "cb6ee2ad-6310-4f91-9653-f7795c279e83" + "label": null, + "output_name": "discarded", + "uuid": "61cb379d-0384-441a-8dc5-d4baf8951f5e" } ] - }, + }, "12": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", - "errors": null, - "id": 12, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", + "errors": null, + "id": 12, "input_connections": { "input_type|fasta_input": { - "id": 4, + "id": 4, "output_name": "output" - }, + }, "input_type|identifiers": { - "id": 11, + "id": 11, "output_name": "ids_lists" } - }, - "inputs": [], - "label": null, - "name": "T-Coffee", + }, + "inputs": [], + "label": null, + "name": "T-Coffee", "outputs": [ { - "name": "fasta_aln", + "name": "fasta_aln", "type": "fasta" } - ], + ], "position": { - "left": 703.890625, - "top": 739.046875 - }, + "bottom": 293.5500030517578, + "height": 144, + "left": 656.88330078125, + "right": 856.88330078125, + "top": 149.5500030517578, + "width": 200, + "x": 656.88330078125, + "y": 149.5500030517578 + }, "post_job_actions": { "HideDatasetActionfasta_aln": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "fasta_aln" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", "tool_shed_repository": { - "changeset_revision": "c67bd5acbae2", - "name": "t_coffee", - "owner": "earlhaminst", + "changeset_revision": "0a189243186d", + "name": "t_coffee", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"outputs\": \"[\\\"fasta_aln\\\"]\", \"__rerun_remap_job_id__\": null, \"input_type\": \"{\\\"__current_case__\\\": 0, \\\"fasta_input\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}, \\\"filter_fasta\\\": \\\"yes\\\", \\\"identifiers\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"method03\": \"null\", \"method02\": \"[\\\"clustalw_msa\\\"]\", \"method01\": \"null\"}", - "tool_version": "11.0.8_1", - "type": "tool", - "uuid": "827ba178-5028-4ae4-b5e1-f234bcfce9f8", + }, + "tool_state": "{\"input_type\": {\"filter_fasta\": \"yes\", \"__current_case__\": 0, \"fasta_input\": {\"__class__\": \"ConnectedValue\"}, \"identifiers\": {\"__class__\": \"ConnectedValue\"}}, \"method01\": null, \"method02\": [\"clustalw_msa\"], \"method03\": null, \"outputs\": [\"fasta_aln\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "11.0.8_1", + "type": "tool", + "uuid": "827ba178-5028-4ae4-b5e1-f234bcfce9f8", "workflow_outputs": [] - }, + }, "13": { - "annotation": "", - "content_id": "trimmer", - "errors": null, - "id": 13, + "annotation": "", + "content_id": "trimmer", + "errors": null, + "id": 13, "input_connections": { "input1": { - "id": 11, + "id": 11, "output_name": "ids_lists" } - }, - "inputs": [], - "label": null, - "name": "Trim", + }, + "inputs": [], + "label": null, + "name": "Trim", "outputs": [ { - "name": "out_file1", + "name": "out_file1", "type": "input" } - ], + ], "position": { - "left": 1537.640625, - "top": 802.59375 - }, + "bottom": 306.3000030517578, + "height": 93.19999694824219, + "left": 1490.63330078125, + "right": 1690.63330078125, + "top": 213.10000610351562, + "width": 200, + "x": 1490.63330078125, + "y": 213.10000610351562 + }, "post_job_actions": { "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "out_file1" } - }, - "tool_id": "trimmer", - "tool_state": "{\"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"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", + }, + "tool_id": "trimmer", + "tool_state": "{\"col\": \"0\", \"end\": \"-2\", \"fastq\": \"\", \"ignore\": null, \"input1\": {\"__class__\": \"ConnectedValue\"}, \"start\": \"1\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.0.2", + "type": "tool", + "uuid": "72a2109e-e01f-466e-a962-5c7ff5d0c2e3", "workflow_outputs": [] - }, + }, "14": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", - "errors": null, - "id": 14, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", + "errors": null, + "id": 14, "input_connections": { "header_criteria|identifiers": { - "id": 13, + "id": 13, "output_name": "out_file1" - }, + }, "input": { - "id": 0, + "id": 0, "output_name": "output" } - }, - "inputs": [], - "label": null, - "name": "Filter FASTA", + }, + "inputs": [], + "label": null, + "name": "Filter FASTA", "outputs": [ { - "name": "output", + "name": "output", "type": "fasta" } - ], + ], "position": { - "left": 1529.78125, - "top": 952.5 - }, + "bottom": 547.8000030517578, + "height": 184.8000030517578, + "left": 1482.7833251953125, + "right": 1682.7833251953125, + "top": 363, + "width": 200, + "x": 1482.7833251953125, + "y": 363 + }, "post_job_actions": { "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "output" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.2", "tool_shed_repository": { - "changeset_revision": "cd22452edec2", - "name": "filter_by_fasta_ids", - "owner": "galaxyp", + "changeset_revision": "cd22452edec2", + "name": "filter_by_fasta_ids", + "owner": "galaxyp", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"dedup\": \"\\\"false\\\"\", \"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"header_criteria\": \"{\\\"__current_case__\\\": 1, \\\"header_criteria_select\\\": \\\"id_list\\\", \\\"id_regex\\\": {\\\"__current_case__\\\": 0, \\\"find\\\": \\\"beginning\\\"}, \\\"identifiers\\\": {\\\"__class__\\\": \\\"ConnectedValue\\\"}}\", \"output_discarded\": \"\\\"false\\\"\", \"sequence_criteria\": \"{\\\"__current_case__\\\": 0, \\\"sequence_criteria_select\\\": \\\"\\\"}\"}", - "tool_version": "2.2", - "type": "tool", - "uuid": "b22832ea-47b0-46a1-87da-e362672133b1", + }, + "tool_state": "{\"dedup\": \"false\", \"header_criteria\": {\"header_criteria_select\": \"id_list\", \"__current_case__\": 1, \"identifiers\": {\"__class__\": \"ConnectedValue\"}, \"id_regex\": {\"find\": \"beginning\", \"__current_case__\": 0}}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"output_discarded\": \"false\", \"sequence_criteria\": {\"sequence_criteria_select\": \"\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2", + "type": "tool", + "uuid": "b22832ea-47b0-46a1-87da-e362672133b1", "workflow_outputs": [] - }, + }, "15": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", - "errors": null, - "id": 15, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", + "errors": null, + "id": 15, "input_connections": { "input1": { - "id": 14, + "id": 14, "output_name": "output" - }, + }, "input2": { - "id": 12, + "id": 12, "output_name": "fasta_aln" } - }, - "inputs": [], - "label": null, - "name": "tranalign", + }, + "inputs": [], + "label": null, + "name": "tranalign", "outputs": [ { - "name": "out_file1", + "name": "out_file1", "type": "fasta" } - ], + ], "position": { - "left": 994.828125, - "top": 1161.484375 - }, + "bottom": 695.5833282470703, + "height": 123.59999084472656, + "left": 947.8333129882812, + "right": 1147.8333129882812, + "top": 571.9833374023438, + "width": 200, + "x": 947.8333129882812, + "y": 571.9833374023438 + }, "post_job_actions": { "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "out_file1" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0", "tool_shed_repository": { - "changeset_revision": "dc492eb6a4fc", - "name": "emboss_5", - "owner": "devteam", + "changeset_revision": "dc492eb6a4fc", + "name": "emboss_5", + "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"input2\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__page__\": null, \"input1\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"out_format1\": \"\\\"fasta\\\"\", \"__rerun_remap_job_id__\": null, \"table\": \"\\\"0\\\"\"}", - "tool_version": "5.0.0", - "type": "tool", - "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", + }, + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"input2\": {\"__class__\": \"ConnectedValue\"}, \"out_format1\": \"fasta\", \"table\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.0.0", + "type": "tool", + "uuid": "e33d053e-1edf-44b7-a08a-abe8e5bcfbc6", "workflow_outputs": [] - }, + }, "16": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0", - "errors": null, - "id": 16, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0", + "errors": null, + "id": 16, "input_connections": { "aln": { - "id": 15, + "id": 15, "output_name": "out_file1" - }, + }, "species_tree": { - "id": 1, + "id": 1, "output_name": "output" } - }, + }, "inputs": [ { - "description": "runtime parameter for tool TreeBeST best", + "description": "runtime parameter for tool TreeBeST best", "name": "C" } - ], - "label": null, - "name": "TreeBeST best", + ], + "label": null, + "name": "TreeBeST best", "outputs": [ { - "name": "output", + "name": "output", "type": "nhx" } - ], + ], "position": { - "left": 1412.875, - "top": 1147.96875 - }, + "bottom": 773.6666870117188, + "height": 215.20001220703125, + "left": 1365.88330078125, + "right": 1565.88330078125, + "top": 558.4666748046875, + "width": 200, + "x": 1365.88330078125, + "y": 558.4666748046875 + }, "post_job_actions": { "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "output" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0", "tool_shed_repository": { - "changeset_revision": "b78b529f66db", - "name": "treebest_best", - "owner": "earlhaminst", + "changeset_revision": "b78b529f66db", + "name": "treebest_best", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"A\": \"\\\"false\\\"\", \"aln\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"C\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"b\": \"\\\"0.01\\\"\", \"d\": \"\\\"0.15\\\"\", \"g\": \"\\\"false\\\"\", \"F\": \"\\\"11\\\"\", \"__page__\": null, \"s\": \"\\\"false\\\"\", \"k\": \"{\\\"__current_case__\\\": 0, \\\"k_selector\\\": \\\"yes\\\"}\", \"c\": \"\\\"2\\\"\", \"L\": \"\\\"0.2\\\"\", \"P\": \"\\\"false\\\"\", \"S\": \"\\\"false\\\"\", \"r\": \"\\\"false\\\"\", \"a\": \"{\\\"__current_case__\\\": 0, \\\"a_selector\\\": \\\"yes\\\"}\", \"species_tree\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"N\": \"\\\"false\\\"\", \"__rerun_remap_job_id__\": null, \"l\": \"\\\"0.1\\\"\"}", - "tool_version": "1.9.2.post0", - "type": "tool", - "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", + }, + "tool_state": "{\"A\": \"false\", \"C\": {\"__class__\": \"RuntimeValue\"}, \"F\": \"11\", \"L\": \"0.2\", \"N\": \"false\", \"P\": \"false\", \"S\": \"false\", \"a\": {\"a_selector\": \"yes\", \"__current_case__\": 0}, \"aln\": {\"__class__\": \"ConnectedValue\"}, \"b\": \"0.01\", \"c\": \"2\", \"d\": \"0.15\", \"g\": \"false\", \"k\": {\"k_selector\": \"yes\", \"__current_case__\": 0}, \"l\": \"0.1\", \"r\": \"false\", \"s\": \"false\", \"species_tree\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.9.2.post0", + "type": "tool", + "uuid": "3e42f4c3-7258-465b-bb24-7ea9e2d3ec40", "workflow_outputs": [] - }, + }, "17": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.1", - "errors": null, - "id": 17, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.2", + "errors": null, + "id": 17, "input_connections": { "genetreeFile": { - "id": 16, + "id": 16, "output_name": "output" } - }, - "inputs": [], - "label": null, - "name": "ETE GeneTree splitter", + }, + "inputs": [ + { + "description": "runtime parameter for tool ETE GeneTree splitter", + "name": "genetreeFile" + } + ], + "label": null, + "name": "ETE GeneTree splitter", "outputs": [ { - "name": "genetrees_lists", + "name": "genetrees_lists", "type": "input" } - ], + ], "position": { - "left": 1908.984375, - "top": 1125.984375 - }, + "bottom": 702.4833374023438, + "height": 134, + "left": 1818.9833984375, + "right": 2018.9833984375, + "top": 568.4833374023438, + "width": 200, + "x": 1818.9833984375, + "y": 568.4833374023438 + }, "post_job_actions": { "HideDatasetActiongenetrees_lists": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "genetrees_lists" } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.1", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.2", "tool_shed_repository": { - "changeset_revision": "6a5282f71f82", - "name": "ete", - "owner": "earlhaminst", + "changeset_revision": "541a2ffc01ff", + "name": "ete", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"genetreeFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"output_format\": \"\\\"9\\\"\", \"gene_node\": \"\\\"0\\\"\", \"gainlose_conditional\": \"{\\\"__current_case__\\\": 0, \\\"gainlose\\\": \\\"False\\\"}\", \"__rerun_remap_job_id__\": null}", - "tool_version": "3.1.1", - "type": "tool", - "uuid": "ca969e72-b56e-44eb-a63e-72125b23f7c9", + }, + "tool_state": "{\"gainlose_conditional\": {\"gainlose\": \"False\", \"__current_case__\": 0}, \"gene_node\": \"0\", \"genetreeFile\": {\"__class__\": \"RuntimeValue\"}, \"output_format\": \"9\", \"splitter\": \"dups\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.1.2", + "type": "tool", + "uuid": "75b554b1-8e1c-4a9b-b74d-952beb61b721", "workflow_outputs": [] - }, + }, "18": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", - "errors": null, - "id": 18, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", + "errors": null, + "id": 18, "input_connections": { "alignmentFile": { - "id": 12, + "id": 12, "output_name": "fasta_aln" - }, + }, "genesFile": { - "id": 2, + "id": 2, "output_name": "output" - }, + }, "treeFile": { - "id": 16, + "id": 16, "output_name": "output" } - }, - "inputs": [], - "label": null, - "name": "Gene Align and Family Aggregator", + }, + "inputs": [], + "label": null, + "name": "Gene Align and Family Aggregator", "outputs": [ { - "name": "outputFile", + "name": "outputFile", "type": "gafa.sqlite" } - ], + ], "position": { - "left": 2184.890625, - "top": 629.96875 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", + "bottom": 255.6666717529297, + "height": 215.20001220703125, + "left": 2137.88330078125, + "right": 2337.88330078125, + "top": 40.46665954589844, + "width": 200, + "x": 2137.88330078125, + "y": 40.46665954589844 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/gafa/gafa/0.3.0", "tool_shed_repository": { - "changeset_revision": "b9f1bcf5ee59", - "name": "gafa", - "owner": "earlhaminst", + "changeset_revision": "b9f1bcf5ee59", + "name": "gafa", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"treeFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"alignmentFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"genesFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\"}", - "tool_version": "0.3.0", - "type": "tool", - "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", + }, + "tool_state": "{\"alignmentFile\": {\"__class__\": \"ConnectedValue\"}, \"genesFile\": {\"__class__\": \"ConnectedValue\"}, \"treeFile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.3.0", + "type": "tool", + "uuid": "049fb5e1-4f3b-4cf5-80a6-2fa609674fc5", "workflow_outputs": [ { - "label": null, - "output_name": "outputFile", - "uuid": "a3dbb7a3-356a-4019-a10d-08896e990c8e" + "label": null, + "output_name": "outputFile", + "uuid": "73f2f8c4-9832-48f8-813a-fd0cbf009204" } ] - }, + }, "19": { - "annotation": "", - "content_id": "__FLATTEN__", - "errors": null, - "id": 19, + "annotation": "", + "content_id": "__FLATTEN__", + "errors": null, + "id": 19, "input_connections": { "input": { - "id": 17, + "id": 17, "output_name": "genetrees_lists" } - }, - "inputs": [], - "label": null, - "name": "Flatten Collection", + }, + "inputs": [], + "label": null, + "name": "Flatten Collection", "outputs": [ { - "name": "output", + "name": "output", "type": "input" } - ], + ], "position": { - "left": 2206.984375, - "top": 1024.96875 - }, + "bottom": 549.0666809082031, + "height": 113.60000610351562, + "left": 2159.9833984375, + "right": 2359.9833984375, + "top": 435.4666748046875, + "width": 200, + "x": 2159.9833984375, + "y": 435.4666748046875 + }, "post_job_actions": { "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "output" } - }, - "tool_id": "__FLATTEN__", - "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"__rerun_remap_job_id__\": null, \"join_identifier\": \"\\\"_\\\"\", \"__page__\": null}", - "tool_version": "1.0.0", - "type": "tool", - "uuid": "5f6a95f6-1036-4a33-b610-a080b971a324", + }, + "tool_id": "__FLATTEN__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"join_identifier\": \"_\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "5f6a95f6-1036-4a33-b610-a080b971a324", "workflow_outputs": [] - }, + }, "20": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_homology_classifier/3.1.1", - "errors": null, - "id": 20, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_homology_classifier/3.1.1", + "errors": null, + "id": 20, "input_connections": { "genetreeFile": { - "id": 19, + "id": 19, "output_name": "output" } - }, - "inputs": [], - "label": null, - "name": "Homology Classifier and Filter", + }, + "inputs": [], + "label": null, + "name": "Homology Classifier and Filter", "outputs": [ { - "name": "homology", + "name": "homology", "type": "tabular" } - ], + ], "position": { - "left": 2341.984375, - "top": 1160.96875 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_homology_classifier/3.1.1", + "bottom": 725.8666839599609, + "height": 154.40000915527344, + "left": 2294.9833984375, + "right": 2494.9833984375, + "top": 571.4666748046875, + "width": 200, + "x": 2294.9833984375, + "y": 571.4666748046875 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_homology_classifier/3.1.1", "tool_shed_repository": { - "changeset_revision": "6a5282f71f82", - "name": "ete", - "owner": "earlhaminst", + "changeset_revision": "b29ee6a16524", + "name": "ete", + "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"genetreeFile\": \"{\\\"__class__\\\": \\\"ConnectedValue\\\"}\", \"format_type\": \"{\\\"__current_case__\\\": 0, \\\"homologies\\\": [\\\"one-to-one\\\", \\\"one-to-many\\\", \\\"many-to-one\\\", \\\"many-to-many\\\", \\\"paralogs\\\"], \\\"out_format\\\": \\\"tabular\\\"}\"}", - "tool_version": "3.1.1", - "type": "tool", - "uuid": "427c5e21-0ed7-41b9-8e2b-447ea99e5c29", + }, + "tool_state": "{\"format_type\": {\"out_format\": \"tabular\", \"__current_case__\": 0, \"homologies\": [\"one-to-one\", \"one-to-many\", \"many-to-one\", \"many-to-many\", \"paralogs\"]}, \"genetreeFile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.1.1", + "type": "tool", + "uuid": "427c5e21-0ed7-41b9-8e2b-447ea99e5c29", "workflow_outputs": [ { - "label": null, - "output_name": "homology", - "uuid": "d20dba82-b0c5-41d7-9f2e-f67240548967" + "label": null, + "output_name": "homology", + "uuid": "470f9126-778c-40bd-93ea-2d0ebfd985d2" + } + ] + }, + "21": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_gene_csv_finder/3.1.2", + "errors": null, + "id": 21, + "input_connections": { + "genetreeFile": { + "id": 19, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Gene Copy Number Finder", + "name": "genetreeFile" + }, + { + "description": "runtime parameter for tool Gene Copy Number Finder", + "name": "speciesorder" + } + ], + "label": null, + "name": "Gene Copy Number Finder", + "outputs": [ + { + "name": "genes", + "type": "tabular" + } + ], + "position": { + "bottom": 918.3999938964844, + "height": 154.39999389648438, + "left": 2312, + "right": 2512, + "top": 764, + "width": 200, + "x": 2312, + "y": 764 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_gene_csv_finder/3.1.2", + "tool_shed_repository": { + "changeset_revision": "dc32007a6b36", + "name": "ete", + "owner": "earlhaminst", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"genetreeFile\": {\"__class__\": \"RuntimeValue\"}, \"speciesorder\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "3.1.2", + "type": "tool", + "uuid": "437d0eeb-8391-49db-99d8-d4e41ee5d9ee", + "workflow_outputs": [ + { + "label": "Gene Copy Number Finder on input dataset(s)", + "output_name": "genes", + "uuid": "96311b11-c446-49c4-8220-b0dacabd2b00" } ] } - }, - "tags": [], - "uuid": "45eedb69-98b5-4ea2-9f17-791fa54ef823", - "version": 20 -} \ No newline at end of file + }, + "tags": [], + "uuid": "c3ff9db2-1e29-4b92-8633-b06eb0973eb4", + "version": 1 +}