Updating workflows/transcriptomics/rnaseq-de from 0.5 to 0.6

Author: planemo-autoupdate

workflows/transcriptomics/rnaseq-de/CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.6] - 2026-01-12
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy2`
+
 ## [0.5] - 2025-12-08
 
 ### Automatic update

workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting.ga

@@ -221,7 +221,7 @@
         },
         "7": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy2",
             "errors": null,
             "id": 7,
             "input_connections": {
@@ -279,16 +279,16 @@
                     "output_name": "deseq_out"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy2",
             "tool_shed_repository": {
-                "changeset_revision": "9a882d108833",
+                "changeset_revision": "6c363db8c702",
                 "name": "deseq2",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"advanced_options\": {\"esf_cond\": {\"esf\": \"\", \"__current_case__\": 0}, \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}, \"use_beta_priors\": false}, \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": [\"pdf\", \"normCounts\"], \"alpha_ma\": {\"__class__\": \"ConnectedValue\"}}, \"select_data\": {\"how\": \"datasets_per_level\", \"__current_case__\": 1, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": \"DEFactor\", \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": \"MainFactor\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}, {\"__index__\": 1, \"factorLevel\": \"BaseFactor\", \"countsFile\": {\"__class__\": \"ConnectedValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
-            "tool_version": "2.11.40.8+galaxy0",
+            "tool_version": "2.11.40.8+galaxy2",
             "type": "tool",
             "uuid": "45883538-b692-4e35-8dee-d08974682a9c",
             "when": null,
@@ -721,12 +721,7 @@
                     "output_name": "output"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Volcano Plot",
-                    "name": "input"
-                }
-            ],
+            "inputs": [],
             "label": "Generate Volcanot plot of DE genes",
             "name": "Volcano Plot",
             "outputs": [
@@ -747,7 +742,7 @@
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"input\": {\"__class__\": \"RuntimeValue\"}, \"labels\": {\"label_select\": \"signif\", \"__current_case__\": 0, \"top_num\": \"10\"}, \"lfc_thresh\": {\"__class__\": \"ConnectedValue\"}, \"out_options\": {\"rscript_out\": false}, \"plot_options\": {\"boxes\": false, \"title\": null, \"xlab\": null, \"ylab\": null, \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"shape_or_facet\": null, \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"with_header\": {\"header\": \"auto\", \"__current_case__\": 0, \"fdr_col\": \"7\", \"pval_col\": \"6\", \"lfc_col\": \"3\", \"label_col\": \"13\", \"shape_col\": null}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"labels\": {\"label_select\": \"signif\", \"__current_case__\": 0, \"top_num\": \"10\"}, \"lfc_thresh\": {\"__class__\": \"ConnectedValue\"}, \"out_options\": {\"rscript_out\": false}, \"plot_options\": {\"boxes\": false, \"title\": null, \"xlab\": null, \"ylab\": null, \"xmin\": null, \"xmax\": null, \"ymax\": null, \"legend\": null, \"legend_labs\": \"Down,Not Sig,Up\"}, \"shape_or_facet\": null, \"signif_thresh\": {\"__class__\": \"ConnectedValue\"}, \"with_header\": {\"header\": \"auto\", \"__current_case__\": 0, \"fdr_col\": \"7\", \"pval_col\": \"6\", \"lfc_col\": \"3\", \"label_col\": \"13\", \"shape_col\": null}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}",
             "tool_uuid": null,
             "tool_version": "4.0.1+galaxy0",
             "type": "tool",
@@ -1063,11 +1058,11 @@
             ]
         }
     },
-    "release": "0.5",
     "tags": [
         "transcriptomics",
         "RNAseq"
     ],
-    "uuid": "7a32e152-5491-461e-8936-2bbbd84baf20",
-    "version": 1
-}
+    "uuid": "2b317c5b-3757-4a0b-9fe3-a2a4db686e9c",
+    "version": 1,
+    "release": "0.6"
+}