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1 <tool id="VarAmpliCNV_MergeCounts" name="Merge Counts" version="0.1.0" >
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2 <requirements>
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3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
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4 </requirements>
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5
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6 <command detect_errors="exit_code"><![CDATA[
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7 mkdir -p infiles
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8
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9 #for $element in $inputFile:
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10 && bname=\$(basename ${element})
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11 && ln -s "${element}" "infiles/\$bname.txt"
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12 #end for
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13
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14 &&
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15
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16 MergeCounts.py -d 'infiles' -o "$outfile"
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17
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18 ]]></command>
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19 <inputs>
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20 <param name="inputFile" type="data" format="txt" optional="false" multiple="True" label="Sample Amplicon Counts" help="This file is created by the VarAmpliCNV 'Count' tool." />
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21 </inputs>
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22 <outputs>
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23 <data name="outfile" format="rdata" label="VarAmpliCNV on ${on_string}: Aggregated Counts" />
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24 </outputs>
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25 <help>
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26 **VarAmpliCNV : Merge Count files**
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27
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28 Merge a list of count files from "varAmpliCNV Count" into a single cohort for CNV-calling.
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29
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30 **Parameters are :**
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31
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32 * Count file (txt) : A list or collection of count files from "varAmpliNCV Count".
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33
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34
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35 **Output files :**
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36
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37 * Count-by-Sample Matrix (Rdata) : Rdata object containing counts for all provided samples.
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38 </help>
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39 </tool>
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