Mercurial > repos > geert-vandeweyer > varamplicnv
comparison varamplicnv-5bafb1c69d03/VarAmpliCNV_MergeCounts.xml @ 0:febc6023d37b draft
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| author | geert-vandeweyer |
|---|---|
| date | Fri, 25 Sep 2020 08:29:36 +0000 |
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| -1:000000000000 | 0:febc6023d37b |
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| 1 <tool id="VarAmpliCNV_MergeCounts" name="Merge Counts" version="0.1.0" > | |
| 2 <requirements> | |
| 3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container> | |
| 4 </requirements> | |
| 5 | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 mkdir -p infiles | |
| 8 | |
| 9 #for $element in $inputFile: | |
| 10 && bname=\$(basename ${element}) | |
| 11 && ln -s "${element}" "infiles/\$bname.txt" | |
| 12 #end for | |
| 13 | |
| 14 && | |
| 15 | |
| 16 MergeCounts.py -d 'infiles' -o "$outfile" | |
| 17 | |
| 18 ]]></command> | |
| 19 <inputs> | |
| 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." /> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data name="outfile" format="rdata" label="VarAmpliCNV on ${on_string}: Aggregated Counts" /> | |
| 24 </outputs> | |
| 25 <help> | |
| 26 **VarAmpliCNV : Merge Count files** | |
| 27 | |
| 28 Merge a list of count files from "varAmpliCNV Count" into a single cohort for CNV-calling. | |
| 29 | |
| 30 **Parameters are :** | |
| 31 | |
| 32 * Count file (txt) : A list or collection of count files from "varAmpliNCV Count". | |
| 33 | |
| 34 | |
| 35 **Output files :** | |
| 36 | |
| 37 * Count-by-Sample Matrix (Rdata) : Rdata object containing counts for all provided samples. | |
| 38 </help> | |
| 39 </tool> |