annotate [APliBio]Nebula tools suite/Nebula/MotifDiscovery/chipmunk.xml @ 1:0ec82f1785af draft

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<tool id="chipmunk_chiphorde" name="ChIPmunk" version="1.0.0">
  <description>De novo motif finding</description>
  <command interpreter="bash">chipmunk.sh -f $inputfile -n $motif_number_selector -m $minw -v $maxw -z $mode -o $log_outfile -p $processed_output -i $image_output -x "$name" -y ${GALAXY_DATA_INDEX_DIR}</command>
  <inputs>
   <param name="name" type="text" value="ChIPseq" label="Name" />
   <param format="fasta" name="inputfile" type="data" label="Sequences"/>
   <param name="motif_number_selector" type="select" label="Number of different motifs to search">
          <option value="1">1</option>
          <option value="2">2</option>
          <option value="3" selected="true">3</option>
          <option value="4">4</option>
   </param>
        
   <param name="minw" type="integer" value="10" label="Min width of motif to search" />
   <param name="maxw" type="integer" value="15" label="Max width of motif to search" />      

   <param name="mode" type="select" label="Mode for additional motif finding" help="use 'mask' to mask already identified motifs in your sequences and 'filter' to filter out the whole sequences with already identified motifs">
          <option value="filter">filter</option>
          <option value="mask" selected="true">mask</option>
   </param>
   </inputs>
  <outputs>
    <data format="log" name="log_outfile" label="row ChIPmunk output for ${name} (log)"/>
    <data format="txt" name="processed_output" label="motifs for ${name}(txt)"/>
    <data format="png" name="image_output" label="motifs for ${name}(png)"/>
  </outputs>
   
  <help>
**What it does**

ChIPmunk detects over-represented non-overlapping motifs in fasta sequences

  </help>
</tool>