Mercurial > repos > enios > nc_rna
view rankprod2.xml @ 15:97abe4dc3ee3 draft
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author | enios |
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date | Sat, 22 May 2021 07:30:24 +0000 |
parents | da21e15c8365 |
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<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 $choose.genes=='T' Rscript /logrankprodf.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes #end if #if $choose.genes=='F' Rscript /logrankprodf.R "c($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>