From 8675cbba9a352a2053f44e651e62525057781630 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Tue, 28 Nov 2023 00:08:25 +0000 Subject: [PATCH 1/2] Updating workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting from 0.3.1 to 0.3.2 --- .../CHANGELOG.md | 6 + .../variation-reporting.ga | 476 +++++++++--------- 2 files changed, 257 insertions(+), 225 deletions(-) diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md index 01047fedc..f7f1325f7 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## [0.3.2] 2023-11-28 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0` was updated to `toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1` + ## [0.3.1] 2023-11-20 - Fix author in dockstore diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga index 2a5047664..626e32912 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga @@ -11,14 +11,41 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis reporting", - "release": "0.3.1", + "release": "0.3.2", "steps": { "0": { - "annotation": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", + "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", "content_id": null, "errors": null, "id": 0, "input_connections": {}, + "inputs": [ + { + "description": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", + "name": "Variation data to report" + } + ], + "label": "Variation data to report", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 10.28125, + "top": 34.08333333333334 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"vcf\", \"vcf_bgzip\"], \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "577438f0-38b1-4fc1-9145-935566d62347", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, "inputs": [ { "description": "Allele Frequency Filter. This is the minimum allele frequency required for variants to be included in the reports.", @@ -29,14 +56,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": -421.578125, - "top": 368.4583333333333 + "left": 5.3125, + "top": 186.91145833333331 }, "tool_id": null, "tool_state": "{\"default\": 0.05, \"parameter_type\": \"float\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "2e5a5b38-c204-45a2-98e2-e113bce5a14b", + "when": null, "workflow_outputs": [ { "label": "af_filter_threshold", @@ -45,11 +73,11 @@ } ] }, - "1": { + "2": { "annotation": "Depth Filter. This is the minimum depth of all alignments at a variant site. ", "content_id": null, "errors": null, - "id": 1, + "id": 2, "input_connections": {}, "inputs": [ { @@ -61,14 +89,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": -426.109375, - "top": 466.4739583333333 + "left": 0.78125, + "top": 284.9270833333333 }, "tool_id": null, "tool_state": "{\"default\": 1, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "c7fc64c7-51c7-465b-9184-ca834d4cf6b2", + "when": null, "workflow_outputs": [ { "label": "dp_filter_threshold", @@ -77,32 +106,6 @@ } ] }, - "2": { - "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", - "content_id": null, - "errors": null, - "id": 2, - "input_connections": {}, - "inputs": [ - { - "description": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", - "name": "Variation data to report" - } - ], - "label": "Variation data to report", - "name": "Input dataset collection", - "outputs": [], - "position": { - "left": -416.609375, - "top": 215.63020833333334 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"vcf\", \"vcf_bgzip\"], \"collection_type\": \"list\"}", - "tool_version": null, - "type": "data_collection_input", - "uuid": "577438f0-38b1-4fc1-9145-935566d62347", - "workflow_outputs": [] - }, "3": { "annotation": "Depth Filter for variant allele. This is the minimum depth of alignments supporting a variant.", "content_id": null, @@ -119,14 +122,15 @@ "name": "Input parameter", "outputs": [], "position": { - "left": -426.890625, - "top": 548.9739583333334 + "left": 0.0, + "top": 367.42708333333337 }, "tool_id": null, "tool_state": "{\"default\": 10, \"parameter_type\": \"integer\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "145bbc55-8893-413d-9620-f3d85e65527a", + "when": null, "workflow_outputs": [ { "label": "dp_alt_filter_threshold", @@ -151,14 +155,15 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 263.125, - "top": 219.95833333333334 + "left": 690.015625, + "top": 38.41145833333334 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"]}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "8b89e674-9012-4f66-a59a-ce05d2fe4223", + "when": null, "workflow_outputs": [] }, "5": { @@ -177,14 +182,15 @@ "name": "Input parameter", "outputs": [], "position": { - 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"tool_state": "{\"advanced\": {\"output_type\": \"svg\", \"ratio\": \"0.67\", \"color\": \"Set3\"}, \"clustering\": {\"do\": \"TRUE\", \"__current_case__\": 0, \"nclust\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"ward.D2\"}, \"sinputs\": {\"__class__\": \"ConnectedValue\"}, \"varfreq\": \"0.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0+galaxy3", + "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.1", "type": "tool", - "uuid": "583b8d59-2cc0-468e-a0b7-3b1a788c7613", + "uuid": "0b2f751b-03c6-4302-9060-16856bb4157c", + "when": null, "workflow_outputs": [ { - "label": "variant_frequency_plot", + "label": "by_variant_report", "output_name": "outfile", - "uuid": "986f1d1a-02c0-4d91-9f6e-a09a088732ee" + "uuid": "bbb19b95-70e3-43fb-baae-525f752b86e9" } ] }, @@ -1579,8 +1607,8 @@ } ], "position": { - "left": 3403.796875, - "top": 512.0989583333334 + "left": 3830.6875, + "top": 330.55208333333337 }, "post_job_actions": { "RenameDatasetActionoutfile": { @@ -1593,15 +1621,16 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", + "changeset_revision": "d698c222f354", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.1", "type": "tool", "uuid": "e55320de-be51-4fa5-908e-76c03de24a77", + "when": null, "workflow_outputs": [ { "label": "combined_variant_report", @@ -1612,53 +1641,50 @@ }, "35": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "errors": null, "id": 35, "input_connections": { - "infile": { - "id": 30, - "output_name": "outfile" + "clustering|nclust": { + "id": 5, + "output_name": "output" + }, + "sinputs": { + "id": 32, + "output_name": "list_output_tab" } }, "inputs": [], "label": null, - "name": "Sort", + "name": "Variant Frequency Plot", "outputs": [ { "name": "outfile", - "type": "input" + "type": "pdf" } ], "position": { - "left": 3400, - "top": 302.4427083333333 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "Combined Variant Report by Variant" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } + "left": 3821.671875, + "top": 596.9895833333334 }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "f46f0e4f75c4", - "name": "text_processing", - "owner": "bgruening", + "changeset_revision": "3d0adeee3f2b", + "name": "snpfreqplot", + "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"header\": \"1\", \"ignore_case\": \"false\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.1", + "tool_state": "{\"advanced\": {\"output_type\": \"svg\", \"ratio\": \"0.67\", \"color\": \"Set3\"}, \"clustering\": {\"do\": \"TRUE\", \"__current_case__\": 0, \"nclust\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"ward.D2\"}, \"sinputs\": {\"__class__\": \"ConnectedValue\"}, \"varfreq\": \"0.0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0+galaxy3", "type": "tool", - "uuid": "0b2f751b-03c6-4302-9060-16856bb4157c", + "uuid": "583b8d59-2cc0-468e-a0b7-3b1a788c7613", + "when": null, "workflow_outputs": [ { - "label": "by_variant_report", + "label": "variant_frequency_plot", "output_name": "outfile", - "uuid": "bbb19b95-70e3-43fb-baae-525f752b86e9" + "uuid": "986f1d1a-02c0-4d91-9f6e-a09a088732ee" } ] } @@ -1668,4 +1694,4 @@ "covid19.galaxyproject.org" ], "uuid": "b08c744d-7c61-4b58-ac5f-4b5886c3c643" -} +} \ No newline at end of file From 202b6cf1340582528227594157865ee8240dbd6e Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Tue, 5 Mar 2024 19:19:53 +0000 Subject: [PATCH 2/2] Updating workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting from 0.3.2 to 0.3.3 --- .../variation-reporting.ga | 302 ++++++++++++++---- 1 file changed, 237 insertions(+), 65 deletions(-) diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga index 626e32912..ffcbe21e9 100644 --- a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "COVID-19: variation analysis reporting", - "release": "0.3.2", + "release": "0.3.3", "steps": { "0": { "annotation": "Variation data in VCF format. Can be the output of any of the workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling", @@ -210,7 +210,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "input" + } + ], "label": null, "name": "SnpSift Filter", "outputs": [ @@ -369,7 +374,20 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "filter_expression" + }, + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "filtering" + }, + { + "description": "runtime parameter for tool SnpSift Filter", + "name": "input" + } + ], "label": null, "name": "SnpSift Filter", "outputs": [ @@ -422,7 +440,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool SnpSift Extract Fields", + "name": "input" + } + ], "label": null, "name": "SnpSift Extract Fields", "outputs": [ @@ -479,7 +502,16 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Replace column", + "name": "original_file" + }, + { + "description": "runtime parameter for tool Replace column", + "name": "replace_information" + } + ], "label": null, "name": "Replace column", "outputs": [ @@ -539,7 +571,12 @@ "output_name": "outfile_replace" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -592,7 +629,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -636,7 +678,7 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", "errors": null, "id": 14, "input_connections": { @@ -645,7 +687,12 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Replace", + "name": "infile" + } + ], "label": null, "name": "Replace", "outputs": [ @@ -667,15 +714,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\t]+\\\\t([^\\\\t,]+),[^\\\\s]+\", \"replace_pattern\": \"\\\\t$1\\\\t$2\\\\t$3\\\\t$4\\\\t$5\\\\t$6\\\\t$7\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": true, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}, {\"__index__\": 1, \"find_pattern\": \"(GroupBy|collapse)\\\\(([^)]+)\\\\)\", \"replace_pattern\": \"$2\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.4", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "25f665b6-2b6a-49a3-a395-29706cd772ab", "when": null, @@ -698,7 +745,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Collapse Collection", + "name": "input_list" + } + ], "label": null, "name": "Collapse Collection", "outputs": [ @@ -743,7 +795,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Compute", + "name": "input" + } + ], "label": null, "name": "Compute", "outputs": [ @@ -779,7 +836,7 @@ }, "17": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", "errors": null, "id": 17, "input_connections": { @@ -788,7 +845,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Replace", + "name": "infile" + } + ], "label": null, "name": "Replace", "outputs": [ @@ -810,15 +872,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"EFF[*].\", \"replace_pattern\": \"\", \"is_regex\": false, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.4", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "82276b6c-5c6e-49eb-8ee5-46041c273d30", "when": null, @@ -841,7 +903,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -886,7 +953,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Filter", + "name": "input" + } + ], "label": null, "name": "Filter", "outputs": [ @@ -925,7 +997,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -968,7 +1045,7 @@ }, "21": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "errors": null, "id": 21, "input_connections": { @@ -981,7 +1058,16 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Join", + "name": "infile1" + }, + { + "description": "runtime parameter for tool Join", + "name": "infile2" + } + ], "label": null, "name": "Join", "outputs": [ @@ -1008,15 +1094,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "7e27aac8-1d1e-4d82-88e3-59c4cd61baeb", "when": null, @@ -1033,7 +1119,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -1078,7 +1169,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -1123,7 +1219,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Datamash", + "name": "in_file" + } + ], "label": null, "name": "Datamash", "outputs": [ @@ -1159,7 +1260,7 @@ }, "25": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "errors": null, "id": 25, "input_connections": { @@ -1172,7 +1273,16 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Join", + "name": "infile1" + }, + { + "description": "runtime parameter for tool Join", + "name": "infile2" + } + ], "label": null, "name": "Join", "outputs": [ @@ -1192,15 +1302,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"3\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "3927af37-c003-4fac-a8af-88ba2b656b22", "when": null, @@ -1208,7 +1318,7 @@ }, "26": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "errors": null, "id": 26, "input_connections": { @@ -1221,7 +1331,16 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Join", + "name": "infile1" + }, + { + "description": "runtime parameter for tool Join", + "name": "infile2" + } + ], "label": null, "name": "Join", "outputs": [ @@ -1241,15 +1360,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"20\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "472af513-7900-41a5-b049-feb2d630ad2c", "when": null, @@ -1266,7 +1385,12 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -1296,7 +1420,7 @@ }, "28": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "errors": null, "id": 28, "input_connections": { @@ -1309,7 +1433,16 @@ "output_name": "out_file" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Join", + "name": "infile1" + }, + { + "description": "runtime parameter for tool Join", + "name": "infile2" + } + ], "label": null, "name": "Join", "outputs": [ @@ -1336,15 +1469,15 @@ "output_name": "output" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"column1\": \"1\", \"column2\": \"1\", \"empty_string_filler\": \"0\", \"header\": true, \"ignore_case\": false, \"infile1\": {\"__class__\": \"ConnectedValue\"}, \"infile2\": {\"__class__\": \"ConnectedValue\"}, \"jointype\": \" \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "1b250a36-d3ae-415e-9764-006182096a60", "when": null, @@ -1361,7 +1494,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -1391,7 +1529,7 @@ }, "30": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", "errors": null, "id": 30, "input_connections": { @@ -1400,7 +1538,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Replace", + "name": "infile" + } + ], "label": null, "name": "Replace", "outputs": [ @@ -1427,15 +1570,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"unique\\\\(Sample\\\\)\\\\tcollapse\\\\(Sample\\\\)\\\\tcollapse\\\\(AF\\\\)\", \"replace_pattern\": \"SAMPLES(above-thresholds)\\\\tSAMPLES(all)\\\\tAFs(all)\", \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.4", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "6116c1c6-7c7c-43fe-9c91-609c91c6ed85", "when": null, @@ -1452,7 +1595,12 @@ "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Cut", + "name": "input" + } + ], "label": null, "name": "Cut", "outputs": [ @@ -1491,7 +1639,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Split file", + "name": "split_parms" + } + ], "label": null, "name": "Split file", "outputs": [ @@ -1535,7 +1688,7 @@ }, "33": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", "errors": null, "id": 33, "input_connections": { @@ -1544,7 +1697,12 @@ "output_name": "outfile" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "infile" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -1566,15 +1724,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"g\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.1", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "0b2f751b-03c6-4302-9060-16856bb4157c", "when": null, @@ -1588,7 +1746,7 @@ }, "34": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", "errors": null, "id": 34, "input_connections": { @@ -1597,7 +1755,12 @@ "output_name": "out_file1" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Sort", + "name": "infile" + } + ], "label": null, "name": "Sort", "outputs": [ @@ -1619,15 +1782,15 @@ "output_name": "outfile" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy0", "tool_shed_repository": { - "changeset_revision": "d698c222f354", + "changeset_revision": "12615d397df7", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"header\": \"1\", \"ignore_case\": false, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"sortkeys\": [{\"__index__\": 0, \"column\": \"1\", \"order\": \"\", \"style\": \"\"}, {\"__index__\": 1, \"column\": \"2\", \"order\": \"\", \"style\": \"n\"}], \"unique\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.1", + "tool_version": "9.3+galaxy0", "type": "tool", "uuid": "e55320de-be51-4fa5-908e-76c03de24a77", "when": null, @@ -1654,7 +1817,16 @@ "output_name": "list_output_tab" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool Variant Frequency Plot", + "name": "clustering" + }, + { + "description": "runtime parameter for tool Variant Frequency Plot", + "name": "sinputs" + } + ], "label": null, "name": "Variant Frequency Plot", "outputs": [