<tool id="rdiff-web" name="rDiff" version="0.3">
    <description>Determines differentially expressed transcripts from read alignments</description>
    <command interpreter="bash"> 
        rdiff_run.sh $test_meth $anno_input $read_length $rdiff_out $rdiff_out.extra_files_path
        #for $i in $replicate_groups
        #for $j in $i.replicates
        $j.bam_alignment?
        #end for
        :
        #end for
        >> $Log_File 
    </command>
  <inputs>

    <!-- genome annotation in GFF format -->
	<param format="gff3" name="anno_input" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>

    <!-- RNA-seq samples and corresponding replicates -->
   <repeat name="replicate_groups" title="Sample" min="2" max="2">
     <repeat name="replicates" title="Replicate">
        <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM is the binary version of the SAM format, a tab-delimited text file that contains sequence alignment data."/>
     </repeat>
   </repeat>

    
     <param name="test_meth" type="select" label="rDiff testing method" help="Statistical test on differential transcript expression data." >
            <option value="poisson">Poisson</option>
            <option value="param">Parametric</option>
            <option value="nonparam">Nonparametric</option>
    </param>
    <param name="read_length" type="text" value="75" help="default 75 nucleotide." label="Read length from sequencing experiment"/>

  </inputs>

  <outputs>
    <data format="txt" name="rdiff_out" label="${tool.name} on ${on_string}: Differential Testing Result" />
    <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/>
  </outputs>
  
  <help>

.. class:: infomark

**What it does** 

rDiff_ is a tool for differential expression testing of RNA-Seq data.

.. _rDiff: http://bioweb.me/rdiff

  </help>
</tool>