Mercurial > repos > iuc > deseq2
changeset 16:a7bf54ecfa9d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7
| author | iuc |
|---|---|
| date | Thu, 22 Sep 2016 05:49:41 -0400 |
| parents | d856341e03c8 |
| children | 24930eeff731 |
| files | deseq2.xml test-data/deseq2_out.tab test-data/deseq2_out_filtered.tab tool_dependencies.xml |
| diffstat | 4 files changed, 6868 insertions(+), 6869 deletions(-) [+] |
line wrap: on
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--- a/deseq2.xml Tue May 31 06:24:39 2016 -0400 +++ b/deseq2.xml Thu Sep 22 05:49:41 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>
--- a/test-data/deseq2_out.tab Tue May 31 06:24:39 2016 -0400 +++ b/test-data/deseq2_out.tab Thu Sep 22 05:49:41 2016 -0400 @@ -1,3062 +1,3179 @@ -FBgn0003360 1933.95040021558 2.83931228953808 0.131427107601069 21.6037036906911 1.65776552489818e-103 4.55056636584551e-100 -FBgn0029167 1648.81894046778 2.12846963025105 0.111026271791993 19.1708646602015 6.48223943041875e-82 8.89687361824973e-79 -FBgn0025111 655.359768612902 -2.5644293647992 0.137667338019513 -18.6277253682041 1.91491281446672e-77 1.75214522523705e-74 -FBgn0029896 211.4755450268 2.08777269052165 0.146415563061924 14.2592265935463 3.92783372063478e-46 2.69547589078562e-43 -FBgn0000071 151.249383869297 -2.07788825355436 0.168180795911583 -12.3550863360568 4.57264975460857e-35 2.5103847152801e-32 -FBgn0027279 1317.42349329018 1.15789519295162 0.0979487508070972 11.8214391037208 3.02458387385013e-32 1.38374712228644e-29 -FBgn0023479 1361.36610109448 1.42278095029403 0.123382436293769 11.5314707103565 9.15659568231105e-31 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--- a/tool_dependencies.xml Tue May 31 06:24:39 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="deseq2" version="1.8.2"> - <repository changeset_revision="81a3e281bf21" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>