Mercurial > repos > arkarachai-fungtammasan > str_fm
changeset 7:90021d286a67 draft
Deleted selected files
author | arkarachai-fungtammasan |
---|---|
date | Mon, 24 Aug 2015 13:45:11 -0400 |
parents | d75894f5d61b |
children | 808bd6c3ac71 |
files | Galaxy-Workflow-microsatellite_profiling.ga test-data/Galaxy-Workflow-microsatellite_profiling.ga |
diffstat | 2 files changed, 0 insertions(+), 1528 deletions(-) [+] |
line wrap: on
line diff
--- a/Galaxy-Workflow-microsatellite_profiling.ga Sat Aug 22 12:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,764 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "Profile length of microsatellites or short tandem repeats from short read data", - "format-version": "0.1", - "name": "microsatellite_profiling", - "steps": { - "0": { - "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", - "name": "single end fastq" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 200, - "top": 274.765625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"single end fastq\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "need to be prepared by user using TR genome profiling", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "need to be prepared by user using TR genome profiling", - "name": "TR in genome" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 177, - "top": 412.953125 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"TR in genome\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", - "name": "error rate file" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1412.875, - "top": 384.671875 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"error rate file\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "filePath": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "Microsatellite detection", - "outputs": [ - { - "name": "stdout", - "type": "tabular" - } - ], - "position": { - "left": 441.953125, - "top": 252 - }, - "post_job_actions": { - "ChangeDatatypeActionstdout": { - "action_arguments": { - "newtype": "tabular" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "stdout" - }, - "RenameDatasetActionstdout": { - "action_arguments": { - "newname": "TR in raw reads" - }, - "action_type": "RenameDatasetAction", - "output_name": "stdout" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatellite/1.0.0", - "tool_state": "{\"__page__\": 0, \"flankSetting\": \"{\\\"noflankdisplay\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"filePath\": \"null\", \"minlength\": \"\\\"5\\\"\", \"hammingThreshold\": \"\\\"0\\\"\", \"period\": \"\\\"1\\\"\", \"surfix\": \"\\\"20\\\"\", \"prefix\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"inputFileSource\": \"{\\\"inputFileType\\\": \\\"fastq\\\", \\\"__current_case__\\\": 3}\", \"partialmotifs\": \"\\\"True\\\"\", \"multipleruns\": \"\\\"True\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": { - "input": { - "id": 3, - "output_name": "stdout" - } - }, - "inputs": [], - "name": "Read name modifier", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 418.484375, - "top": 385.03125 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/space2underscore_readname/1.0.0", - "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"6\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "microsat_in_read": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "Fetch flanking bases", - "outputs": [ - { - "name": "Leftflanking", - "type": "fastq" - }, - { - "name": "Rightflanking", - "type": "fastq" - } - ], - "position": { - "left": 390.9375, - "top": 509.046875 - }, - "post_job_actions": { - "ChangeDatatypeActionLeftflanking": { - "action_arguments": { - "newtype": "fastqsanger" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "Leftflanking" - }, - "ChangeDatatypeActionRightflanking": { - "action_arguments": { - "newtype": "fastqsanger" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "Rightflanking" - }, - "HideDatasetActionLeftflanking": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "Leftflanking" - }, - "HideDatasetActionRightflanking": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "Rightflanking" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/fetchflank/1.0.0", - "tool_state": "{\"qualitycutoff\": \"\\\"20\\\"\", \"lengthofbasetocheckquality\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"microsat_in_read\": \"null\", \"__page__\": 0}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "this tool has problems with parameter setting when you run it from pipeline. If you want different parameter, it's recommend that you clone pipleline and modify it.", - "id": 6, - "input_connections": { - "paired|input1": { - "id": 5, - "output_name": "Leftflanking" - }, - "paired|input2": { - "id": 5, - "output_name": "Rightflanking" - } - }, - "inputs": [], - "name": "Map with BWA for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - } - ], - "position": { - "left": 403, - "top": 686 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", - "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"outputTopN\\\": \\\"3\\\", \\\"suboptAlign\\\": \\\"\\\", \\\"gapOpenPenalty\\\": \\\"11\\\", \\\"maxGapOpens\\\": \\\"1\\\", \\\"mismatchPenalty\\\": \\\"3\\\", \\\"fracMissingAligns\\\": \\\"0.04\\\", \\\"disallowIndel\\\": \\\"5\\\", \\\"outputTopNDisc\\\": \\\"10\\\", \\\"disallowLongDel\\\": \\\"16\\\", \\\"readGroup\\\": {\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}, \\\"maxInsertSize\\\": \\\"500\\\", \\\"__current_case__\\\": 1, \\\"maxEditDist\\\": \\\"0\\\", \\\"gapExtensPenalty\\\": \\\"4\\\", \\\"maxGapExtens\\\": \\\"-1\\\", \\\"maxEditDistSeed\\\": \\\"2\\\", \\\"noIterSearch\\\": \\\"False\\\", \\\"seed\\\": \\\"-1\\\", \\\"maxOccurPairing\\\": \\\"100000\\\", \\\"source_select\\\": \\\"full\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}", - "tool_version": "1.2.3", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "input1": { - "id": 6, - "output_name": "output" - } - }, - "inputs": [], - "name": "Filter SAM", - "outputs": [ - { - "name": "out_file1", - "type": "sam" - } - ], - "position": { - "left": 778, - "top": 489.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"bits\": \"[{\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 0, \\\"flags\\\": \\\"--0x0004\\\"}]\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "remove all mapped read with soft mask", - "id": 8, - "input_connections": { - "input": { - "id": 7, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Filter", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 781.5, - "top": 602 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Filter1", - "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c6.count('S')==0\\\"\", \"__page__\": 0}", - "tool_version": "1.1.0", - "type": "tool", - "user_outputs": [] - }, - "9": { - "annotation": "", - "id": 9, - "input_connections": { - "input": { - "id": 8, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Sort", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 777.5, - "top": 739 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "sort1", - "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", - "tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - }, - "10": { - "annotation": "", - "id": 10, - "input_connections": { - "flankedbasesSAM": { - "id": 9, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Combine mapped flaked bases", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 723.328125, - "top": 887.828125 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/PEsortedSAM2readprofile/1.0.0", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"maxoriginalreadlength\": \"\\\"101\\\"\", \"maxTRlength\": \"\\\"100\\\"\", \"flankedbasesSAM\": \"null\", \"twobitref\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "11": { - "annotation": "", - "id": 11, - "input_connections": { - "input1": { - "id": 4, - "output_name": "output" - }, - "input2": { - "id": 10, - "output_name": "output" - } - }, - "inputs": [], - "name": "Join two Datasets", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1116.375, - "top": 431.84375 - }, - "post_job_actions": { - "ColumnSetActionout_file1": { - "action_arguments": { - "chromCol": "10", - "endCol": "14", - "nameCol": "", - "startCol": "13", - "strandCol": "" - }, - "action_type": "ColumnSetAction", - "output_name": "out_file1" - }, - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "join1", - "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\"}", - "tool_version": "2.0.2", - "type": "tool", - "user_outputs": [] - }, - "12": { - "annotation": "", - "id": 12, - "input_connections": { - "input1": { - "id": 1, - "output_name": "output" - }, - "input2": { - "id": 11, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Join", - "outputs": [ - { - "name": "output", - "type": "interval" - } - ], - "position": { - "left": 1113.96875, - "top": 560.296875 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0", - "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"fill\": \"\\\"none\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "13": { - "annotation": "", - "id": 13, - "input_connections": { - "input": { - "id": 12, - "output_name": "output" - } - }, - "inputs": [], - "name": "Check microsatellites motif compatibility", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 1122.328125, - "top": 710.84375 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatcompat/1.0.0", - "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"column1\": \"\\\"4\\\"\", \"column2\": \"\\\"10\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "14": { - "annotation": "", - "id": 14, - "input_connections": { - "input": { - "id": 13, - "output_name": "output" - } - }, - "inputs": [], - "name": "Select uninterrupted microsatellites", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 1131.21875, - "top": 852.90625 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatpurity/1.0.0", - "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"period\": \"\\\"1\\\"\", \"input\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "15": { - "annotation": "", - "id": 15, - "input_connections": { - "input": { - "id": 14, - "output_name": "output" - } - }, - "inputs": [], - "name": "Cut", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 1161, - "top": 963.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c5,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "1.0.2", - "type": "tool", - "user_outputs": [] - }, - "16": { - "annotation": "", - "id": 16, - "input_connections": { - "input": { - "id": 15, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Add column", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1168, - "top": 1069.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "addValue", - "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"_\\\"\", \"iterate\": \"\\\"no\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "17": { - "annotation": "", - "id": 17, - "input_connections": { - "input1": { - "id": 16, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Merge Columns", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 1175, - "top": 1184.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "mergeCols1", - "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"columns\": \"[{\\\"__index__\\\": 0, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}}, {\\\"__index__\\\": 1, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}}, {\\\"__index__\\\": 2, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}}]\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "18": { - "annotation": "", - "id": 18, - "input_connections": { - "input1": { - "id": 17, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Group", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 1175, - "top": 1297.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Grouping1", - "tool_state": "{\"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"cat\\\", \\\"opround\\\": \\\"no\\\"}, {\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"4\\\"}, \\\"__index__\\\": 1, \\\"optype\\\": \\\"cat_uniq\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}", - "tool_version": "2.1.0", - "type": "tool", - "user_outputs": [] - }, - "19": { - "annotation": "", - "id": 19, - "input_connections": { - "input": { - "id": 18, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Filter", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1186, - "top": 1405.953125 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "TR profile" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Filter1", - "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c2.count(\\\\\\\",\\\\\\\")>=4\\\"\", \"__page__\": 0}", - "tool_version": "1.1.0", - "type": "tool", - "user_outputs": [] - }, - "20": { - "annotation": "", - "id": 20, - "input_connections": { - "microsat_error_profile": { - "id": 2, - "output_name": "output" - }, - "microsat_raw": { - "id": 19, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Correct genotype for microsatellite errors", - "outputs": [ - { - "name": "microsat_corrected", - "type": "tabular" - } - ], - "position": { - "left": 1591.328125, - "top": 456.8125 - }, - "post_job_actions": { - "RenameDatasetActionmicrosat_corrected": { - "action_arguments": { - "newname": "Genotype file" - }, - "action_type": "RenameDatasetAction", - "output_name": "microsat_corrected" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/GenotypeSTR/2.0.0", - "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}", - "tool_version": "2.0.0", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file
--- a/test-data/Galaxy-Workflow-microsatellite_profiling.ga Sat Aug 22 12:13:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,764 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "Profile length of microsatellites or short tandem repeats from short read data", - "format-version": "0.1", - "name": "microsatellite_profiling", - "steps": { - "0": { - "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites", - "name": "single end fastq" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 249, - "top": 274.765625 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"single end fastq\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "annotation": "need to be prepared by user using TR genome profiling", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "need to be prepared by user using TR genome profiling", - "name": "STR in genome" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 226, - "top": 412.953125 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"STR in genome\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files", - "name": "error rate file" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1492.875, - "top": 497.671875 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"error rate file\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "3": { - "annotation": "", - "id": 3, - "input_connections": { - "filePath": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "STR detection", - "outputs": [ - { - "name": "stdout", - "type": "tabular" - } - ], - "position": { - "left": 515, - "top": 256.5 - }, - "post_job_actions": { - "ChangeDatatypeActionstdout": { - "action_arguments": { - "newtype": "tabular" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "stdout" - }, - "RenameDatasetActionstdout": { - "action_arguments": { - "newname": "STR in raw reads" - }, - "action_type": "RenameDatasetAction", - "output_name": "stdout" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatellite/1.0.0", - "tool_state": "{\"__page__\": 0, \"flankSetting\": \"{\\\"noflankdisplay\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"filePath\": \"null\", \"minlength\": \"\\\"5\\\"\", \"hammingThreshold\": \"\\\"0\\\"\", \"period\": \"\\\"1\\\"\", \"surfix\": \"\\\"20\\\"\", \"prefix\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"inputFileSource\": \"{\\\"inputFileType\\\": \\\"fasta\\\", \\\"__current_case__\\\": 2}\", \"partialmotifs\": \"\\\"True\\\"\", \"multipleruns\": \"\\\"True\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "4": { - "annotation": "", - "id": 4, - "input_connections": { - "input": { - "id": 3, - "output_name": "stdout" - } - }, - "inputs": [], - "name": "Read name modifier", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 478, - "top": 370 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/space2underscore_readname/1.0.0", - "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"6\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "", - "id": 5, - "input_connections": { - "microsat_in_read": { - "id": 4, - "output_name": "output" - } - }, - "inputs": [], - "name": "Fetch bases flanking", - "outputs": [ - { - "name": "Leftflanking", - "type": "fastq" - }, - { - "name": "Rightflanking", - "type": "fastq" - } - ], - "position": { - "left": 446.5, - "top": 503.5 - }, - "post_job_actions": { - "ChangeDatatypeActionLeftflanking": { - "action_arguments": { - "newtype": "fastqsanger" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "Leftflanking" - }, - "ChangeDatatypeActionRightflanking": { - "action_arguments": { - "newtype": "fastqsanger" - }, - "action_type": "ChangeDatatypeAction", - "output_name": "Rightflanking" - }, - "HideDatasetActionLeftflanking": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "Leftflanking" - }, - "HideDatasetActionRightflanking": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "Rightflanking" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/fetchflank/1.0.0", - "tool_state": "{\"qualitycutoff\": \"\\\"20\\\"\", \"lengthofbasetocheckquality\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"microsat_in_read\": \"null\", \"__page__\": 0}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "this tool has problems with parameter setting when you run it from pipeline. If you want different parameter, it's recommend that you clone pipleline and modify it.", - "id": 6, - "input_connections": { - "paired|input1": { - "id": 5, - "output_name": "Leftflanking" - }, - "paired|input2": { - "id": 5, - "output_name": "Rightflanking" - } - }, - "inputs": [], - "name": "Map with BWA for Illumina", - "outputs": [ - { - "name": "output", - "type": "sam" - } - ], - "position": { - "left": 452, - "top": 686 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3", - "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"outputTopN\\\": \\\"3\\\", \\\"suboptAlign\\\": \\\"\\\", \\\"gapOpenPenalty\\\": \\\"11\\\", \\\"maxGapOpens\\\": \\\"1\\\", \\\"mismatchPenalty\\\": \\\"3\\\", \\\"fracMissingAligns\\\": \\\"0.04\\\", \\\"disallowIndel\\\": \\\"5\\\", \\\"outputTopNDisc\\\": \\\"10\\\", \\\"disallowLongDel\\\": \\\"16\\\", \\\"readGroup\\\": {\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}, \\\"maxInsertSize\\\": \\\"500\\\", \\\"__current_case__\\\": 1, \\\"maxEditDist\\\": \\\"0\\\", \\\"gapExtensPenalty\\\": \\\"4\\\", \\\"maxGapExtens\\\": \\\"-1\\\", \\\"maxEditDistSeed\\\": \\\"2\\\", \\\"noIterSearch\\\": \\\"False\\\", \\\"seed\\\": \\\"-1\\\", \\\"maxOccurPairing\\\": \\\"100000\\\", \\\"source_select\\\": \\\"full\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}", - "tool_version": "1.2.3", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "", - "id": 7, - "input_connections": { - "input1": { - "id": 6, - "output_name": "output" - } - }, - "inputs": [], - "name": "Filter SAM", - "outputs": [ - { - "name": "out_file1", - "type": "sam" - } - ], - "position": { - "left": 827, - "top": 489.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"bits\": \"[{\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 0, \\\"flags\\\": \\\"--0x0004\\\"}]\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "remove all mapped read with soft mask", - "id": 8, - "input_connections": { - "input": { - "id": 7, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Filter", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 830.5, - "top": 602 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Filter1", - "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c6.count('S')==0\\\"\", \"__page__\": 0}", - "tool_version": "1.1.0", - "type": "tool", - "user_outputs": [] - }, - "9": { - "annotation": "", - "id": 9, - "input_connections": { - "input": { - "id": 8, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Sort", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 826.5, - "top": 739 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "sort1", - "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}", - "tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - }, - "10": { - "annotation": "", - "id": 10, - "input_connections": { - "flankedbasesSAM": { - "id": 9, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Combine mapped faux paired-end reads", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 757, - "top": 866.5 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/PEsortedSAM2readprofile/1.0.0", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"maxoriginalreadlength\": \"\\\"101\\\"\", \"maxTRlength\": \"\\\"100\\\"\", \"flankedbasesSAM\": \"null\", \"twobitref\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "11": { - "annotation": "", - "id": 11, - "input_connections": { - "input1": { - "id": 4, - "output_name": "output" - }, - "input2": { - "id": 10, - "output_name": "output" - } - }, - "inputs": [], - "name": "Join two Datasets", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1165.375, - "top": 431.84375 - }, - "post_job_actions": { - "ColumnSetActionout_file1": { - "action_arguments": { - "chromCol": "10", - "endCol": "14", - "nameCol": "", - "startCol": "13", - "strandCol": "" - }, - "action_type": "ColumnSetAction", - "output_name": "out_file1" - }, - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "join1", - "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\"}", - "tool_version": "2.0.2", - "type": "tool", - "user_outputs": [] - }, - "12": { - "annotation": "", - "id": 12, - "input_connections": { - "input1": { - "id": 1, - "output_name": "output" - }, - "input2": { - "id": 11, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Join", - "outputs": [ - { - "name": "output", - "type": "interval" - } - ], - "position": { - "left": 1162.96875, - "top": 560.296875 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0", - "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"min\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"fill\": \"\\\"none\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "13": { - "annotation": "", - "id": 13, - "input_connections": { - "input": { - "id": 12, - "output_name": "output" - } - }, - "inputs": [], - "name": "Check STR motif compatibility between reference and read STRs", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 1166.5, - "top": 707.5 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatcompat/1.0.0", - "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"column1\": \"\\\"4\\\"\", \"column2\": \"\\\"10\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "14": { - "annotation": "", - "id": 14, - "input_connections": { - "input": { - "id": 13, - "output_name": "output" - } - }, - "inputs": [], - "name": "Select uninterrupted STRs", - "outputs": [ - { - "name": "output", - "type": "tabular" - } - ], - "position": { - "left": 1203.5, - "top": 836.5 - }, - "post_job_actions": { - "HideDatasetActionoutput": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "output" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/microsatpurity/1.0.0", - "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"period\": \"\\\"1\\\"\", \"input\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "15": { - "annotation": "", - "id": 15, - "input_connections": { - "input": { - "id": 14, - "output_name": "output" - } - }, - "inputs": [], - "name": "Cut", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 1210, - "top": 963.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Cut1", - "tool_state": "{\"columnList\": \"\\\"c1,c2,c3,c4,c5,c7\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", - "tool_version": "1.0.2", - "type": "tool", - "user_outputs": [] - }, - "16": { - "annotation": "", - "id": 16, - "input_connections": { - "input": { - "id": 15, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Add column", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1217, - "top": 1069.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "addValue", - "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"_\\\"\", \"iterate\": \"\\\"no\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "17": { - "annotation": "", - "id": 17, - "input_connections": { - "input1": { - "id": 16, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Merge Columns", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 1224, - "top": 1184.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "mergeCols1", - "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"columns\": \"[{\\\"__index__\\\": 0, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}}, {\\\"__index__\\\": 1, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"7\\\"}}, {\\\"__index__\\\": 2, \\\"datacol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}}]\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "18": { - "annotation": "", - "id": 18, - "input_connections": { - "input1": { - "id": 17, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Group", - "outputs": [ - { - "name": "out_file1", - "type": "tabular" - } - ], - "position": { - "left": 1224, - "top": 1297.953125 - }, - "post_job_actions": { - "HideDatasetActionout_file1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Grouping1", - "tool_state": "{\"operations\": \"[{\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"__index__\\\": 0, \\\"optype\\\": \\\"cat\\\", \\\"opround\\\": \\\"no\\\"}, {\\\"opcol\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"4\\\"}, \\\"__index__\\\": 1, \\\"optype\\\": \\\"cat_uniq\\\", \\\"opround\\\": \\\"no\\\"}]\", \"__page__\": 0, \"input1\": \"null\", \"ignorelines\": \"null\", \"groupcol\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"8\\\"}\", \"__rerun_remap_job_id__\": null, \"ignorecase\": \"\\\"False\\\"\"}", - "tool_version": "2.1.0", - "type": "tool", - "user_outputs": [] - }, - "19": { - "annotation": "", - "id": 19, - "input_connections": { - "input": { - "id": 18, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Filter", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1227, - "top": 1406.953125 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "STR profile" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Filter1", - "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c2.count(\\\\\\\",\\\\\\\")>=4\\\"\", \"__page__\": 0}", - "tool_version": "1.1.0", - "type": "tool", - "user_outputs": [] - }, - "20": { - "annotation": "", - "id": 20, - "input_connections": { - "microsat_error_profile": { - "id": 2, - "output_name": "output" - }, - "microsat_raw": { - "id": 19, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "Correct genotype for STR errors", - "outputs": [ - { - "name": "microsat_corrected", - "type": "tabular" - } - ], - "position": { - "left": 1673.5, - "top": 561.5 - }, - "post_job_actions": { - "RenameDatasetActionmicrosat_corrected": { - "action_arguments": { - "newname": "Genotype file" - }, - "action_type": "RenameDatasetAction", - "output_name": "microsat_corrected" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/str_fm/GenotypeSTR/2.0.0", - "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}", - "tool_version": "2.0.0", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file