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comparison edger.xml @ 1:c469357cf454 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78
author iuc
date Tue, 30 Jan 2018 04:06:46 -0500
parents 1844cd48af49
children 3de72f1f78aa
comparison
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0:1844cd48af49 1:c469357cf454
1 <tool id="edger" name="edgeR" version="3.16.5"> 1 <tool id="edger" name="edgeR" version="3.20.7.0">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> 7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
8 <requirement type="package" version="0.2.15">r-rjson</requirement> 8 <requirement type="package" version="0.2.15">r-rjson</requirement>
9 <requirement type="package" version="1.20.0">r-getopt</requirement> 9 <requirement type="package" version="1.20.0">r-getopt</requirement>
10 <requirement type="package" version="1.4.30">r-statmod</requirement>
10 <!-- required for alpha function used with plotMD --> 11 <!-- required for alpha function used with plotMD -->
11 <requirement type="package" version="0.4.1">r-scales</requirement> 12 <requirement type="package" version="0.5.0">r-scales</requirement>
12 <!-- This should be in limma conda now - check why still needed? -->
13 <requirement type="package" version="1.4.30">r-statmod</requirement>
14 </requirements> 13 </requirements>
15 14
16 <version_command><![CDATA[ 15 <version_command><![CDATA[
17 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: ") 16 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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
18 ]]></version_command> 17 ]]></version_command>
19 18
20 <command detect_errors="exit_code"><![CDATA[ 19 <command detect_errors="exit_code"><![CDATA[
21 #import json 20 #import json
22 Rscript '$__tool_directory__/edger.R' 21 Rscript '$__tool_directory__/edger.R'