From c7b4786d387e9531ee8080aaf5775436ce623bd0 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 18 Nov 2024 05:34:41 +0000
Subject: [PATCH] Updating
 workflows/scRNAseq/pseudobulk-worflow-decoupler-edger from 0.1 to 0.2

---
 .../CHANGELOG.md                              |  5 +++++
 .../pseudo-bulk_edgeR.ga                      | 21 +++++++------------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/CHANGELOG.md b/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/CHANGELOG.md
index 47bbdc1d6..a09144076 100644
--- a/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/CHANGELOG.md
+++ b/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/CHANGELOG.md
@@ -1,4 +1,9 @@
 # Changelog
 
+## [0.2] 2024-11-18
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy5` was updated to `toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8`
+
 ## [0.1] 2024-10-14
 First release.
\ No newline at end of file
diff --git a/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR.ga b/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR.ga
index af193d2ca..24d6e3b7c 100644
--- a/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR.ga
+++ b/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR.ga
@@ -21,7 +21,7 @@
     ],
     "format-version": "0.1",
     "license": "CC-BY-4.0",
-    "release": "0.1",
+    "release": "0.2",
     "name": "Differential gene expression for single-cell data using pseudo-bulk counts with edgeR",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -287,7 +287,7 @@
         },
         "8": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy5",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8",
             "errors": null,
             "id": 8,
             "input_connections": {
@@ -366,15 +366,15 @@
                     "output_name": "samples_metadata"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy5",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8",
             "tool_shed_repository": {
-                "changeset_revision": "f6040492b499",
+                "changeset_revision": "ef054892d47f",
                 "name": "decoupler_pseudobulk",
                 "owner": "ebi-gxa",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"adata_obs_fields_to_merge\": {\"__class__\": \"ConnectedValue\"}, \"factor_fields\": {\"__class__\": \"ConnectedValue\"}, \"filter_expr\": true, \"filter_per_contrast\": {\"filter\": \"no\", \"__current_case__\": 1}, \"groupby\": {\"__class__\": \"ConnectedValue\"}, \"input_file\": {\"__class__\": \"ConnectedValue\"}, \"layer\": {\"__class__\": \"ConnectedValue\"}, \"min_cells\": \"10\", \"min_counts\": \"10\", \"min_counts_per_sample\": \"20\", \"min_total_counts\": \"1000\", \"mode\": \"sum\", \"plot_filtering_figsize\": \"13 13\", \"plot_samples_figsize\": \"13 13\", \"produce_anndata\": false, \"produce_plots\": true, \"sample_key\": {\"__class__\": \"ConnectedValue\"}, \"use_raw\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "1.4.0+galaxy5",
+            "tool_version": "1.4.0+galaxy8",
             "type": "tool",
             "uuid": "12b43361-2dbc-4dd5-89c9-6a9842bb1531",
             "when": null,
@@ -618,12 +618,7 @@
                     "output_name": "outfile"
                 }
             },
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool Text reformatting",
-                    "name": "infile"
-                }
-            ],
+            "inputs": [],
             "label": null,
             "name": "Text reformatting",
             "outputs": [
@@ -644,7 +639,7 @@
                 "owner": "bgruening",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
-            "tool_state": "{\"code\": \"BEGIN { print \\\"header\\\" } NR > 1 { if (!seen[$2]++) words[++count]=$2 } END { for (i=1; i<=count; i++) for (j=i+1; j<=count; j++) print words[i]\\\"-\\\"words[j] }\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_state": "{\"code\": \"BEGIN { print \\\"header\\\" } NR > 1 { if (!seen[$2]++) words[++count]=$2 } END { for (i=1; i<=count; i++) for (j=i+1; j<=count; j++) print words[i]\\\"-\\\"words[j] }\", \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
             "tool_version": "9.3+galaxy1",
             "type": "tool",
             "uuid": "5701bab4-15b7-401a-9689-c127d17e5bdf",
@@ -1020,4 +1015,4 @@
     "tags": [],
     "uuid": "e4e4055c-7e3f-4014-a8e6-343199fd9b01",
     "version": 31
-}
+}
\ No newline at end of file