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comparison deseq2.xml @ 5:4ba2afa87fce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 80abc96e451fb55175aedf74bf90a9196172d4d2-dirty
author iuc
date Fri, 04 Sep 2015 08:26:02 -0400
parents 1ae1da9a5e66
children 982bd8bfa44c
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4:070614c08a94 5:4ba2afa87fce
1 <tool id="deseq2" name="DESeq2" version="2.1.8.0"> 1 <tool id="deseq2" name="DESeq2" version="2.1.8.0">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <requirements> 3 <requirements>
4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> 4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
5 <requirement type="package" version="3.2.1">R</requirement> 5 <requirement type="package" version="3.2.1">R</requirement>
6 <requirement type="package" version="3.10.2">atlas</requirement>
6 <requirement type="package" version="1.8.1">deseq2</requirement> 7 <requirement type="package" version="1.8.1">deseq2</requirement>
7 </requirements> 8 </requirements>
8 <version_command> 9 <version_command>
9 <![CDATA[ 10 <![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) ; 11 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) ;
12 ]]> 13 ]]>
13 </version_command> 14 </version_command>
14 <command interpreter="Rscript"> 15 <command interpreter="Rscript">
15 <![CDATA[ 16 <![CDATA[
16 #import json 17 #import json
17 deseq2.R 18 \$DESEQ2_ROOT_PATH/inst/script/deseq2.R
18 -o "$deseq_out" 19 -o "$deseq_out"
19 #if $pdf: 20 #if $pdf:
20 -p "$plots" 21 -p "$plots"
21 #end if 22 #end if
22 #set $temp_factor_names = list() 23 #set $temp_factor_names = list()