Merge pull request galaxyproject#484 from planemo-autoupdate/workflow…

…s/epigenetics/chipseq-sr Updating workflows/epigenetics/chipseq-sr from 0.11 to 0.12
planemo-autoupdate · Sep 24, 2024 · 260c1db · 260c1db
2 parents 008bce2 + 654212a
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diff --git a/workflows/epigenetics/chipseq-sr/CHANGELOG.md b/workflows/epigenetics/chipseq-sr/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.12] 2024-09-23
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1`
+- `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`
+
 ## [0.11] 2024-07-15
 
 ### Automatic update

diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml b/workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml
@@ -22,27 +22,11 @@
         - that: "has_text"
           text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
     'MultiQC on input dataset(s): Stats':
-      element_tests:
-        bowtie2:
-          asserts:
-            has_text: 
-              text: "49251\t49251\t805"
-        cutadapt:
-          asserts:
-            has_text:
-              text: "4.9\t50000\t587\t749\t49251"
-        general_stats:
-          asserts:
-            has_text_matching: 
-              expression: "200.0\t0.0\t4\t98.[0-9]*\t4.612745098039215"
-        macs:
-          asserts:
-            has_text:
-              text: "4\t49.0\t44078.0\t44038.0\t1.0\t0.0\t200.0"
-        sources:
-          asserts:
-            has_n_lines: 
-              n: 3
+      asserts:
+        has_line:
+          line: "Sample	MACS2_mqc_generalstats_macs2_d	MACS2_mqc_generalstats_macs2_treatment_redundant_rate	MACS2_mqc_generalstats_macs2_peak_count	Bowtie 2 / HiSAT2_mqc_generalstats_bowtie_2_hisat2_overall_alignment_rate	Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"
+        has_text_matching:
+          expression: "wt_H3K4me3\t200.0\t0.0\t4\t98.[0-9]*\t4.6[0-9]*"
     filtered BAM:
       element_tests:
         wt_H3K4me3:

diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr.ga b/workflows/epigenetics/chipseq-sr/chipseq-sr.ga
@@ -10,7 +10,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.11",
+    "release": "0.12",
     "name": "ChIPseq_SR",
     "steps": {
         "0": {
@@ -150,7 +150,7 @@
         },
         "5": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1",
             "errors": null,
             "id": 5,
             "input_connections": {
@@ -204,15 +204,15 @@
                     "output_name": "report"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "aa784cb3810d",
+                "changeset_revision": "5eb7e84243f2",
                 "name": "cutadapt",
                 "owner": "lparsons",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": []}}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "4.9+galaxy0",
+            "tool_version": "4.9+galaxy1",
             "type": "tool",
             "uuid": "c7846b4c-54fb-458e-982e-c0d8358a9f5d",
             "when": null,
@@ -547,7 +547,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "fbf99087e067",
+                "changeset_revision": "86755160afbf",
                 "name": "text_processing",
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -614,7 +614,7 @@
         },
         "11": {
             "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": 11,
             "input_connections": {
@@ -635,17 +635,17 @@
             "label": "MultiQC",
             "name": "MultiQC",
             "outputs": [
-                {
-                    "name": "stats",
-                    "type": "input"
-                },
                 {
                     "name": "plots",
                     "type": "input"
                 },
                 {
                     "name": "html_report",
                     "type": "html"
+                },
+                {
+                    "name": "stats",
+                    "type": "tabular"
                 }
             ],
             "position": {
@@ -659,15 +659,15 @@
                     "output_name": "plots"
                 }
             },
-            "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\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"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\": true, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"bowtie2\", \"__current_case__\": 3, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"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": "fb066848-43df-412a-9767-9613bac7d961",
             "when": null,