From 486e5c76719c682f8cde308a823662bfd52693a5 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 22 Jun 2026 00:28:19 +0000
Subject: [PATCH 1/2] Updating tools/bioconductor-scp from version 1.16.0 to
 1.20.0

---
 tools/bioconductor-scp/bioconductor_scp.xml | 12 ++++++------
 tools/bioconductor-scp/macros.xml           |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/bioconductor-scp/bioconductor_scp.xml b/tools/bioconductor-scp/bioconductor_scp.xml
index 461580a3..d1ee8d48 100644
--- a/tools/bioconductor-scp/bioconductor_scp.xml
+++ b/tools/bioconductor-scp/bioconductor_scp.xml
@@ -9,12 +9,12 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-scp</requirement>
-        <requirement type="package" version="3.54.0">bioconductor-sva</requirement>
-        <requirement type="package" version="1.80.0">bioconductor-impute</requirement>
-        <requirement type="package" version="1.34.0">bioconductor-scater</requirement>
-        <requirement type="package" version="1.16.0">bioconductor-qfeatures</requirement>
-        <requirement type="package" version="3.62.1">bioconductor-limma</requirement>
-        <requirement type="package" version="3.5.1">r-ggplot2</requirement>
+        <requirement type="package" version="3.58.0">bioconductor-sva</requirement>
+        <requirement type="package" version="1.84.0">bioconductor-impute</requirement>
+        <requirement type="package" version="1.38.0">bioconductor-scater</requirement>
+        <requirement type="package" version="1.20.0">bioconductor-qfeatures</requirement>
+        <requirement type="package" version="3.66.0">bioconductor-limma</requirement>
+        <requirement type="package" version="4.0.3">r-ggplot2</requirement>
     </requirements>
     <required_files>
         <include path="utils.r" />
diff --git a/tools/bioconductor-scp/macros.xml b/tools/bioconductor-scp/macros.xml
index 8355a84a..4c5484b0 100644
--- a/tools/bioconductor-scp/macros.xml
+++ b/tools/bioconductor-scp/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.16.0</token>
+    <token name="@TOOL_VERSION@">1.20.0</token>
     <xml name="creator">
         <creator>
             <person

From 1cb4b6e059b3c4574a6b1b45b3beccd9d5fe14bc Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Wed, 22 Jul 2026 13:56:10 +0200
Subject: [PATCH 2/2] updated dependencies

---
 tools/bioconductor-scp/bioconductor_scp.xml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/tools/bioconductor-scp/bioconductor_scp.xml b/tools/bioconductor-scp/bioconductor_scp.xml
index d1ee8d48..7fb9b948 100644
--- a/tools/bioconductor-scp/bioconductor_scp.xml
+++ b/tools/bioconductor-scp/bioconductor_scp.xml
@@ -9,18 +9,15 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-scp</requirement>
-        <requirement type="package" version="3.58.0">bioconductor-sva</requirement>
         <requirement type="package" version="1.84.0">bioconductor-impute</requirement>
+        <requirement type="package" version="3.54.0">bioconductor-sva</requirement>
         <requirement type="package" version="1.38.0">bioconductor-scater</requirement>
-        <requirement type="package" version="1.20.0">bioconductor-qfeatures</requirement>
-        <requirement type="package" version="3.66.0">bioconductor-limma</requirement>
-        <requirement type="package" version="4.0.3">r-ggplot2</requirement>
     </requirements>
     <required_files>
         <include path="utils.r" />
     </required_files>
     <expand macro="creator" />
-    <command detect_errors="exit_code"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
     echo ${run_script} &&
     Rscript  -e 'source("${__tool_directory__}/utils.r")' -e 'source("${run_script}")'
     #if $data_export.export_R_script
@@ -29,6 +26,8 @@
     ]]></command>
     <configfiles>
         <configfile name="run_script"><![CDATA[
+        options(error = function() traceback(3))
+        
         data_input <- read.delim("$input_data", sep="\t")
         metadata <- read.delim("$input_annotations", sep="\t")
         runCol <- colnames(data_input)[$runcol]
@@ -145,7 +144,7 @@
             SummarizedExperiment::colData(scp)[["MedianRI"]] <- medians
 
             #if $generate_QC_plots
-            QC_medianRI <- SummarizedExperimentcolData(scp) |>
+            QC_medianRI <- SummarizedExperiment::colData(scp) |>
                             data.frame() |>
                             ggplot2::ggplot() +
                             ggplot2::aes(x = MedianRI,