Mercurial > repos > enios > birna
comparison rankprod2.xml @ 0:af56c00711c3 draft default tip
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| author | enios |
|---|---|
| date | Wed, 21 Apr 2021 15:09:25 +0000 |
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| children |
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| -1:000000000000 | 0:af56c00711c3 |
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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 $choose.genes=='T' | |
| 11 Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes | |
| 12 #end if | |
| 13 #if $choose.genes=='F' | |
| 14 Rscript /logrankprod.R "c($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> |