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