diff deseq2.xml @ 5:d38fd393402e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit da90fed6a52526d14b5e58fc3c5e7e8448d783d7

--- 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>