From a0babe034dfe4e0f59eab199e06ac246f599ee01 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 13 Jan 2025 04:25:46 +0000
Subject: [PATCH] Updating tools/edger from version 3.36.0 to 4.4.0

---
 tools/edger/edger.xml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/tools/edger/edger.xml b/tools/edger/edger.xml
index 4370eeef452..5f777fa7bf7 100644
--- a/tools/edger/edger.xml
+++ b/tools/edger/edger.xml
@@ -3,8 +3,8 @@
         Perform differential expression of count data
     </description>
     <macros>
-        <token name="@TOOL_VERSION@">3.36.0</token>
-        <token name="@VERSION_SUFFIX@">5</token>
+        <token name="@TOOL_VERSION@">4.4.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <edam_topics>
         <edam_topic>topic_3308</edam_topic>
@@ -19,12 +19,12 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-edger</requirement>
-        <requirement type="package" version="3.50.0">bioconductor-limma</requirement>
-        <requirement type="package" version="0.2.20">r-rjson</requirement>
-        <requirement type="package" version="1.20.3">r-getopt</requirement>
-        <requirement type="package" version="1.4.36">r-statmod</requirement>
+        <requirement type="package" version="3.62.1">bioconductor-limma</requirement>
+        <requirement type="package" version="0.2.23">r-rjson</requirement>
+        <requirement type="package" version="1.20.4">r-getopt</requirement>
+        <requirement type="package" version="1.5.0">r-statmod</requirement>
         <!-- required for alpha function used with plotMD -->
-        <requirement type="package" version="1.1.1">r-scales</requirement>
+        <requirement type="package" version="1.3.0">r-scales</requirement>
     </requirements>
     <version_command><![CDATA[
 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")