--- a/rankprod2.xml	Wed Apr 21 10:09:28 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<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>