comparison rankprod2.xml @ 13:da21e15c8365 draft

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author enios
date Sat, 22 May 2021 07:29:45 +0000
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1 <tool id="rankprodthree" name="RankProd" >
2 <requirements>
3 <container type="docker">bianca7/lncrna:rankprod</container>
4 </requirements>
5 <description>Differential expression with RankProd</description>
6 <stdio>
7 <exit_code range="1:" level="fatal" />
8 </stdio>
9 <command><![CDATA[
10 #if $choose.genes=='T'
11 Rscript /logrankprodf.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes
12 #end if
13 #if $choose.genes=='F'
14 Rscript /logrankprodf.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.method $choose.cutoff
15 #end if
16 ]]></command>
17 <inputs>
18 <param format="tabular, txt" name="file1" type="data" label="input matrix" />
19 <param name="whichcols" type="text" label="Comma separated fields for columns, like 1,2,3,4" />
20 <param name="sc" type="integer" value="1" label="Choose col class" />
21 <param format="tabular, txt" name="file2" type="data" label="input samples matrix" />
22 <param name="whichrows" type="text" label="Comma separated fields for rows" />
23 <param name="norm" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are counts normalized?" />
24 <param name="base" type="select" label="Choose log base" >
25 <option value="2">2</option>
26 <option value="10">10</option>
27 </param>
28 <param name="log" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are they logarithmically transformed?" />
29 <conditional name="choose" >
30 <param name="genes" type="boolean" truevalue="T" falsevalue="F" checked="no" label="Select specific genes or choose method" />
31 <when value="T">
32 <param name="numgenes" type="integer" value="10" label="How many genes" />
33 </when>
34 <when value="F">
35 <param name="method" type="select" label="Select method" >
36 <option value="pfp">pfp</option>
37 <option value="pval">pval</option>
38 </param>
39 <param name="cutoff" type="float" value="0.05" label="Choose cutoff" />
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <data format="txt" name="file3" label="Differentially expressed molecules"/>
45 </outputs>
46 </tool>