<tool id="test_argument" name="test_argu" version="1.0.0">
  <description>To test the arguments from shell.</description>
  <command> 
../testArgu.sh $test_out 
#for $i in $replicate_groups
#for $j in $i.replicates
$j.bam_alignment:#slurp
#end for
#end for
    >> $Log_File </command>
  <inputs>
	<param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
   <repeat name="replicate_groups" title="Replicate group" min="2">
     <repeat name="replicates" title="Replicate">
      <param format="fastq" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/>
     </repeat>
   </repeat>
  </inputs>

  <outputs>
    <data format="txt" name="test_out" label="DESeq result"/>
	<data format="txt" name="Log_File" label="DESeq result"/>
  </outputs>
</tool>