diff varamplicnv-5bafb1c69d03/VarAmpliCNV_MergeCounts.xml @ 1:5c324f9a4e20 draft default tip

Uploaded

--- 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>