diff edger.xml @ 1:2a16413ec60d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78

--- a/edger.xml	Tue Nov 07 08:18:14 2017 -0500
+++ b/edger.xml	Tue Jan 30 04:07:08 2018 -0500
@@ -1,20 +1,19 @@
-<tool id="edger" name="edgeR" version="3.16.5">
+<tool id="edger" name="edgeR" version="3.20.7.0">
     <description>
         Perform differential expression of count data
     </description>
 
     <requirements>
-        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
+        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
         <requirement type="package" version="0.2.15">r-rjson</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.4.30">r-statmod</requirement>
         <!-- required for alpha function used with plotMD -->
-        <requirement type="package" version="0.4.1">r-scales</requirement>
-        <!-- This should be in limma conda now - check why still needed? -->
-        <requirement type="package" version="1.4.30">r-statmod</requirement>
+        <requirement type="package" version="0.5.0">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: ")", 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: ")
+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: ")", 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: ")
     ]]></version_command>
 
     <command detect_errors="exit_code"><![CDATA[