From fe9d31431a084ef569cf015e53c5fd5d93ae6605 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Tue, 24 Sep 2024 14:00:59 +0000 Subject: [PATCH] Updating workflows/epigenetics/consensus-peaks from 1.1 to 1.2 --- .../epigenetics/consensus-peaks/CHANGELOG.md | 10 +++++ .../consensus-peaks-atac-cutandrun.ga | 42 +++++++++---------- .../consensus-peaks-chip-pe.ga | 42 +++++++++---------- .../consensus-peaks-chip-sr.ga | 42 +++++++++---------- 4 files changed, 73 insertions(+), 63 deletions(-) diff --git a/workflows/epigenetics/consensus-peaks/CHANGELOG.md b/workflows/epigenetics/consensus-peaks/CHANGELOG.md index 11d873533..82540217e 100644 --- a/workflows/epigenetics/consensus-peaks/CHANGELOG.md +++ b/workflows/epigenetics/consensus-peaks/CHANGELOG.md @@ -1,5 +1,15 @@ # Changelog +## [1.2] 2024-09-24 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` + ## [1.1] 2024-05-27 ### Automatic update diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga index aea947871..7afaa8136 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ATAC or CUTandRUN replicates", "steps": { "0": { @@ -239,7 +239,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 5, "input_connections": { @@ -268,15 +268,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "9cff58b2-123e-42df-b562-3b2a4a553934", "when": null, @@ -886,7 +886,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -989,7 +989,7 @@ }, "20": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 20, "input_connections": { @@ -1022,15 +1022,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "36713e3f-6110-41f7-8df1-9a9966400fab", "when": null, @@ -1226,7 +1226,7 @@ }, "24": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 24, "input_connections": { @@ -1243,13 +1243,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1263,15 +1263,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1403,7 +1403,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga index 40fa85952..6a069cc8e 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ChIP_PE replicates", "steps": { "0": { @@ -194,7 +194,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -223,15 +223,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "a864ff43-af08-436a-aa78-54491ff0cce6", "when": null, @@ -841,7 +841,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -944,7 +944,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 19, "input_connections": { @@ -977,15 +977,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "ae46e826-d985-4437-abae-152b6877eea7", "when": null, @@ -1136,7 +1136,7 @@ }, "22": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 22, "input_connections": { @@ -1153,13 +1153,13 @@ "label": "multiQC", "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -1173,15 +1173,15 @@ "output_name": "stats" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "abfd8a6544d7", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1313,7 +1313,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga index 05c3c38a5..857414f3b 100644 --- a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga +++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr.ga @@ -81,7 +81,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "1.1", + "release": "1.2", "name": "Get Confident Peaks From ChIP_SR replicates", "steps": { "0": { @@ -194,7 +194,7 @@ }, "4": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 4, "input_connections": { @@ -223,15 +223,15 @@ "output_name": "outputcnt" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - "changeset_revision": "6be888be75f9", + "changeset_revision": "32dc5f781059", "name": "samtools_view", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"all_reads\", \"__current_case__\": 0, \"output_options\": {\"reads_report_type\": \"count\", \"__current_case__\": 1}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.15.1+galaxy2", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "a864ff43-af08-436a-aa78-54491ff0cce6", "when": null, @@ -841,7 +841,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -944,7 +944,7 @@ }, "19": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "errors": null, "id": 19, "input_connections": { @@ -977,15 +977,15 @@ "output_name": "outputsam" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3", "tool_shed_repository": { - 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"tool_version": "1.15.1+galaxy2", + "tool_state": "{\"addref_cond\": {\"addref_select\": \"no\", \"__current_case__\": 0}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"mode\": {\"outtype\": \"selected_reads\", \"__current_case__\": 1, \"filter_config\": {\"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"cond_rg\": {\"select_rg\": \"no\", \"__current_case__\": 0}, \"cond_expr\": {\"select_expr\": \"no\", \"__current_case__\": 0}, \"quality\": null, \"library\": null, \"cigarcons\": null, \"inclusive_filter\": null, \"exclusive_filter\": null, \"exclusive_filter_all\": null, \"tag\": null, \"qname_file\": {\"__class__\": \"RuntimeValue\"}}, \"subsample_config\": {\"subsampling_mode\": {\"select_subsample\": \"target\", \"__current_case__\": 1, \"target\": {\"__class__\": \"ConnectedValue\"}, \"seed\": \"1\"}}, \"output_options\": {\"reads_report_type\": \"retained\", \"__current_case__\": 0, \"complementary_output\": false, \"adv_output\": {\"readtags\": [], \"collapsecigar\": false}, \"output_format\": {\"oformat\": \"bam\", \"__current_case__\": 2}}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.20+galaxy3", "type": "tool", "uuid": "ae46e826-d985-4437-abae-152b6877eea7", "when": null, @@ -1136,7 +1136,7 @@ }, "22": { "annotation": "", - 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"tool_version": "1.11+galaxy1", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"macs2\", \"__current_case__\": 16, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "f7d74248-16e3-4020-8156-caae0e7682ef", "when": null, @@ -1313,7 +1313,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1", "tool_shed_repository": { - "changeset_revision": "fbf99087e067", + "changeset_revision": "86755160afbf", "name": "text_processing", "owner": "bgruening", "tool_shed": "toolshed.g2.bx.psu.edu"