Mercurial > repos > iuc > deseq2

diff deseq2.xml @ 2:9c706d3721ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 521ea70d49fee701db4d832823644c8c3050f8f2-dirty
author iuc
date Fri, 04 Sep 2015 07:11:53 -0400
parents 5b1ce9db498e
children 1ae1da9a5e66
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line diff
--- a/deseq2.xml	Sun Jul 26 14:33:36 2015 -0400
+++ b/deseq2.xml	Fri Sep 04 07:11:53 2015 -0400
@@ -5,7 +5,14 @@
         <requirement type="package" version="3.1.0">R</requirement>
         <requirement type="package" version="1.8.1">deseq2</requirement>
     </requirements>
+    <version_command>
+    <![CDATA[
+        echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) &&
+        cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+    ]]>
+    </version_command>
     <command interpreter="Rscript">
+    <![CDATA[
         #import json
         deseq2.R
             -o "$deseq_out"
@@ -35,6 +42,7 @@
             #if $many_contrasts:
                 -m
             #end if
+    ]]>
     </command>
     <stdio>
         <regex match="Execution halted"
@@ -119,7 +127,7 @@
         </test>
     </tests>
     <help>
-
+<![CDATA[
 .. class:: infomark
 
 **What it does** 
@@ -167,7 +175,7 @@
 
 
 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
-
+]]>
     </help>
     <citations>
         <citation type="doi">10.1186/s13059-014-0550-8</citation>