Mercurial > repos > iuc > deseq2
diff deseq2.xml @ 5:d38fd393402e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
| author | iuc |
|---|---|
| date | Thu, 22 Sep 2016 05:49:52 -0400 |
| parents | 8702e49e68b6 |
| children | 4939397c4706 |
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--- a/deseq2.xml Tue May 31 06:23:49 2016 -0400 +++ b/deseq2.xml Thu Sep 22 05:49:52 2016 -0400 @@ -1,8 +1,11 @@ -<tool id="deseq2" name="DESeq2" version="2.1.8.3"> +<tool id="deseq2" name="DESeq2" version="2.1.8.4"> <description>Determines differentially expressed features from count tables</description> <requirements> <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> - <requirement type="package" version="1.8.2">deseq2</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="2.17.0">r-gplots</requirement> + <requirement type="package" version="0.2.15">r-rjson</requirement> + <requirement type="package" version="1.10.1">bioconductor-deseq2</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -25,8 +28,10 @@ </version_command> <command> <![CDATA[ + R -e 'library(DESeq2); sink("DESEQ2_ROOT_PATH"); cat(file.path(find.package("DESeq2"),"script","deseq2.R"))' && + #import json - Rscript \$DESEQ2_ROOT_PATH/DESeq2/script/deseq2.R + Rscript \$(cat DESEQ2_ROOT_PATH) -o "$deseq_out" #if $pdf: -p "$plots" @@ -128,8 +133,8 @@ </repeat> </repeat> <param name="pdf" value="no"/> - <output name="deseq_out" file="deseq2_out.tab"/> - <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/> + <output name="deseq_out" file="deseq2_out.tab" compare="sim_size" delta="1000"/> + <output name="deseq_out_filtered" file="deseq2_out_filtered.tab" compare="sim_size" delta="1000"/> </test> </tests> <help>