# HG changeset patch
# User biancakrieger
# Date 1618998984 0
# Node ID 48f8c22771357e9e5ce9bf8b16bff3907e9e283c
# Parent  53c5e6332601aa1823b020faa898fbff8a0030c0
Uploaded

diff -r 53c5e6332601 -r 48f8c2277135 rankprod2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rankprod2.xml	Wed Apr 21 09:56:24 2021 +0000
@@ -0,0 +1,46 @@
+<tool id="rankprodthree" name="RankProd" >
+ <requirements>
+     <container type="docker">bianca7/lncrna:rankprod</container>
+ </requirements>
+ <description>Differential expression with RankProd</description>
+ <stdio>
+   <exit_code range="1:" level="fatal" />
+ </stdio>
+ <command><![CDATA[
+       #if $choose.genes=='T'
+      Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes
+     #end if
+     #if $choose.genes=='F'
+      Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.method $choose.cutoff
+     #end if
+  ]]></command>
+  <inputs>
+   <param format="tabular, txt" name="file1" type="data" label="input matrix" />
+   <param name="whichcols" type="text" label="Comma separated fields for columns, like 1,2,3,4" />
+   <param name="sc" type="integer" value="1" label="Choose col class" />
+   <param format="tabular, txt" name="file2" type="data" label="input samples matrix" />
+   <param name="whichrows" type="text" label="Comma separated fields for rows" />
+   <param name="norm" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are counts normalized?" />
+   <param name="base" type="select" label="Choose log base" >
+     <option value="2">2</option>
+     <option value="10">10</option>
+   </param>
+   <param name="log" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are they logarithmically transformed?" />
+   <conditional name="choose" >
+     <param name="genes" type="boolean" truevalue="T" falsevalue="F" checked="no" label="Select specific genes or choose method" />
+     <when value="T">
+       <param name="numgenes" type="integer" value="10" label="How many genes" />
+     </when>
+     <when value="F">
+       <param name="method" type="select" label="Select method" >
+        <option value="pfp">pfp</option>
+        <option value="pval">pval</option>
+       </param>
+       <param name="cutoff" type="float" value="0.05" label="Choose cutoff" />
+     </when>
+   </conditional>
+ </inputs>
+ <outputs>
+    <data format="txt" name="file3" label="Differentially expressed molecules"/>
+ </outputs>
+</tool>