Mercurial > repos > geert-vandeweyer > varamplicnv
diff varamplicnv-5bafb1c69d03/VarAmpliCNV_MergeCounts.xml @ 1:5c324f9a4e20 draft default tip
Uploaded
author | geert-vandeweyer |
---|---|
date | Fri, 25 Sep 2020 08:30:57 +0000 |
parents | febc6023d37b |
children |
line wrap: on
line diff
--- a/varamplicnv-5bafb1c69d03/VarAmpliCNV_MergeCounts.xml Fri Sep 25 08:29:36 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<tool id="VarAmpliCNV_MergeCounts" name="Merge Counts" version="0.1.0" > - <requirements> - <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container> - </requirements> - - <command detect_errors="exit_code"><![CDATA[ - mkdir -p infiles - - #for $element in $inputFile: - && bname=\$(basename ${element}) - && ln -s "${element}" "infiles/\$bname.txt" - #end for - - && - - MergeCounts.py -d 'infiles' -o "$outfile" - - ]]></command> - <inputs> - <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." /> - </inputs> - <outputs> - <data name="outfile" format="rdata" label="VarAmpliCNV on ${on_string}: Aggregated Counts" /> - </outputs> - <help> -**VarAmpliCNV : Merge Count files** - -Merge a list of count files from "varAmpliCNV Count" into a single cohort for CNV-calling. - -**Parameters are :** - -* Count file (txt) : A list or collection of count files from "varAmpliNCV Count". - - -**Output files :** - -* Count-by-Sample Matrix (Rdata) : Rdata object containing counts for all provided samples. - </help> -</tool>