jianma committed 0d44a34

add a tool to convert cel version

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Files changed (2)


     <tool file="filters/gtf2bedgraph.xml" />
     <tool file="filters/wig_to_bigwig.xml" />
     <tool file="filters/bed_to_bigbed.xml" />
+    <tool file="filters/cel_conversion.xml" />
   <section name="Extract Features" id="features">
     <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />


+<tool name="CEL conversion" id="cel_conversion" version="1.0.0">
+    <description>convert cel files to xda cel format</description>
+    <command interpreter="command">/bin/bash $shscript</command>
+    <inputs>
+      <param format="cel" name="celfile" type="data" label="Input cel file to be converted" />
+    </inputs>
+    <outputs>
+      <data format="cel" name="outcelfile" label="Output CEL file in xda format" />
+      <data format="txt" name="log" label="CEL file convert log." />
+    </outputs>
+    <configfiles>
+      <configfile name="shscript">
+#import os
+#set filename = os.path.join("output", os.path.split($celfile)[-1])
+apt-cel-convert  -f xda -o ./output $celfile
+cp output/apt-cel-convert.log $log
+cp $filename $outcelfile
+      </configfile>
+    </configfiles>
+    <help>
+    </help>
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