Mercurial > repos > earlhaminst > geneseqtofamily
view 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 source
{ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", "name": "GeneSeqToFamily", "steps": { "0": { "annotation": "", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "CDS" } ], "label": "CDS", "name": "Input dataset", "outputs": [], "position": { "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": {}, "inputs": [ { "description": "", "name": "Species tree" } ], "label": "Species tree", "name": "Input dataset", "outputs": [], "position": { "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": {}, "inputs": [ { "description": "", "name": "Gene feature information" } ], "label": "Gene feature information", "name": "Input dataset", "outputs": [], "position": { "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, "input_connections": { "input1": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "transeq", "outputs": [ { "name": "out_file1", "type": "fasta" } ], "position": { "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", "output_name": "out_file1" } }, "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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, "input_connections": { "input": { "id": 3, "output_name": "out_file1" } }, "inputs": [], "label": null, "name": "Filter FASTA", "outputs": [ { "name": "output", "type": "fasta" }, { "name": "discarded", "type": "fasta" } ], "position": { "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", "output_name": "discarded" }, "HideDatasetActionoutput": { "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" } }, "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": "c877294f8025", "name": "ncbi_blast_plus", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": [] }, "6": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332", "errors": null, "id": 6, "input_connections": { "input": { "id": 4, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool faSplit", "name": "O" } ], "label": null, "name": "faSplit", "outputs": [ { "name": "output_list", "type": "input" } ], "position": { "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", "output_name": "output_list" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/332", "tool_shed_repository": { "changeset_revision": "dc36d50254d8", "name": "ucsc_fasplit", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": [] }, "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": 5, "output_name": "outfile" }, "query": { "id": 6, "output_name": "output_list" } }, "inputs": [], "label": null, "name": "NCBI BLAST+ blastp", "outputs": [ { "name": "output1", "type": "tabular" } ], "position": { "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", "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" } }, "inputs": [], "label": null, "name": "Concatenate datasets", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "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", "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" } }, "inputs": [], "label": null, "name": "BLAST parser", "outputs": [ { "name": "output", "type": "tabular" } ], "position": { "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": "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, "input_connections": { "inputFile": { "id": 9, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool hcluster_sg", "name": "c_conditional" } ], "label": null, "name": "hcluster_sg", "outputs": [ { "name": "outputFile", "type": "tabular" } ], "position": { "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": "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, "input_connections": { "inputFile": { "id": 10, "output_name": "outputFile" } }, "inputs": [], "label": null, "name": "hcluster_sg parser", "outputs": [ { "name": "ids_lists", "type": "input" }, { "name": "discarded", "type": "txt" } ], "position": { "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", "output_name": "ids_lists" } }, "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": "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, "input_connections": { "input_type|fasta_input": { "id": 4, "output_name": "output" }, "input_type|identifiers": { "id": 11, "output_name": "ids_lists" } }, "inputs": [], "label": null, "name": "T-Coffee", "outputs": [ { "name": "fasta_aln", "type": "fasta" } ], "position": { "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", "output_name": "fasta_aln" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8_1", "tool_shed_repository": { "changeset_revision": "0a189243186d", "name": "t_coffee", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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, "input_connections": { "input1": { "id": 11, "output_name": "ids_lists" } }, "inputs": [], "label": null, "name": "Trim", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "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", "output_name": "out_file1" } }, "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, "input_connections": { "header_criteria|identifiers": { "id": 13, "output_name": "out_file1" }, "input": { "id": 0, "output_name": "output" } }, "inputs": [], "label": null, "name": "Filter FASTA", "outputs": [ { "name": "output", "type": "fasta" } ], "position": { "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", "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\": \"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, "input_connections": { "input1": { "id": 14, "output_name": "output" }, "input2": { "id": 12, "output_name": "fasta_aln" } }, "inputs": [], "label": null, "name": "tranalign", "outputs": [ { "name": "out_file1", "type": "fasta" } ], "position": { "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", "output_name": "out_file1" } }, "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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, "input_connections": { "aln": { "id": 15, "output_name": "out_file1" }, "species_tree": { "id": 1, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool TreeBeST best", "name": "C" } ], "label": null, "name": "TreeBeST best", "outputs": [ { "name": "output", "type": "nhx" } ], "position": { "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", "output_name": "output" } }, "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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/3.1.2", "errors": null, "id": 17, "input_connections": { "genetreeFile": { "id": 16, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool ETE GeneTree splitter", "name": "genetreeFile" } ], "label": null, "name": "ETE GeneTree splitter", "outputs": [ { "name": "genetrees_lists", "type": "input" } ], "position": { "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", "output_name": "genetrees_lists" } }, "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_genetree_splitter/3.1.2", "tool_shed_repository": { "changeset_revision": "541a2ffc01ff", "name": "ete", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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, "input_connections": { "alignmentFile": { "id": 12, "output_name": "fasta_aln" }, "genesFile": { "id": 2, "output_name": "output" }, "treeFile": { "id": 16, "output_name": "output" } }, "inputs": [], "label": null, "name": "Gene Align and Family Aggregator", "outputs": [ { "name": "outputFile", "type": "gafa.sqlite" } ], "position": { "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", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": "73f2f8c4-9832-48f8-813a-fd0cbf009204" } ] }, "19": { "annotation": "", "content_id": "__FLATTEN__", "errors": null, "id": 19, "input_connections": { "input": { "id": 17, "output_name": "genetrees_lists" } }, "inputs": [], "label": null, "name": "Flatten Collection", "outputs": [ { "name": "output", "type": "input" } ], "position": { "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", "output_name": "output" } }, "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, "input_connections": { "genetreeFile": { "id": 19, "output_name": "output" } }, "inputs": [], "label": null, "name": "Homology Classifier and Filter", "outputs": [ { "name": "homology", "type": "tabular" } ], "position": { "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": "b29ee6a16524", "name": "ete", "owner": "earlhaminst", "tool_shed": "toolshed.g2.bx.psu.edu" }, "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": "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": "c3ff9db2-1e29-4b92-8633-b06eb0973eb4", "version": 1 }