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comparison deseq2.xml @ 16:a7bf54ecfa9d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
author iuc
date Thu, 22 Sep 2016 05:49:41 -0400
parents d856341e03c8
children 24930eeff731
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15:d856341e03c8 16:a7bf54ecfa9d
1 <tool id="deseq2" name="DESeq2" version="2.1.8.3"> 1 <tool id="deseq2" name="DESeq2" version="2.1.8.4">
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="1.8.2">deseq2</requirement> 5 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="2.17.0">r-gplots</requirement>
7 <requirement type="package" version="0.2.15">r-rjson</requirement>
8 <requirement type="package" version="1.10.1">bioconductor-deseq2</requirement>
6 </requirements> 9 </requirements>
7 <stdio> 10 <stdio>
8 <regex match="Execution halted" 11 <regex match="Execution halted"
9 source="both" 12 source="both"
10 level="fatal" 13 level="fatal"
23 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 26 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
24 ]]> 27 ]]>
25 </version_command> 28 </version_command>
26 <command> 29 <command>
27 <![CDATA[ 30 <![CDATA[
31 R -e 'library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))' &&
32
28 #import json 33 #import json
29 Rscript \$DESEQ2_ROOT_PATH/DESeq2/script/deseq2.R 34 Rscript \$(cat DESEQ2_ROOT_PATH)
30 -o "$deseq_out" 35 -o "$deseq_out"
31 #if $pdf: 36 #if $pdf:
32 -p "$plots" 37 -p "$plots"
33 #end if 38 #end if
34 #set $temp_factor_names = list() 39 #set $temp_factor_names = list()
126 <param name="factorLevel" value="Untreated"/> 131 <param name="factorLevel" value="Untreated"/>
127 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> 132 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
128 </repeat> 133 </repeat>
129 </repeat> 134 </repeat>
130 <param name="pdf" value="no"/> 135 <param name="pdf" value="no"/>
131 <output name="deseq_out" file="deseq2_out.tab"/> 136 <output name="deseq_out" file="deseq2_out.tab" compare="sim_size" delta="1000"/>
132 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/> 137 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab" compare="sim_size" delta="1000"/>
133 </test> 138 </test>
134 </tests> 139 </tests>
135 <help> 140 <help>
136 <![CDATA[ 141 <![CDATA[
137 .. class:: infomark 142 .. class:: infomark