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Cistrome-Harvard-dev2 / tools / filters / cel_conversions.xml

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<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="txt" name="log" label="CEL file convert log." />
      <data format="cel" name="celoutput" label="output CEL xda format" />
    </outputs>
    <configfiles>
      <configfile name="shscript">
#!/bin/bash
#import os

#set $dollar = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)

#set $path = $os.path.abspath($__app__.config.tool_path)
#set $prog = os.path.join($path, "filters", "cel_conversions.py")
#echo $prog
#echo $celfile
python $prog -i $celfile -o $celoutput ${ad}${gt} $log
###import os
###set $filename = os.path.join("output", os.path.basename(str($celfile)))
##echo $filename
##mkdir output
##apt-cel-convert  -f xda -o output "$celfile"
###cp output/apt-cel-convert.log $log
###cp $filename $outcelfile

      </configfile>
    </configfiles>
    <help>
uu
    </help>
</tool>