<tool id="chromeister" name="Chromeister">
   <description>A heuristic approach for ultra fast previsualization of pairwise genome comparisons</description>
   <inputs>
      <param name="query" type="data" format="fasta" label="Query sequence" help="Query sequence file in fasta format" />
      <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference sequence file in fasta format" />
      <param name="dimension" type="integer" value="1000" label="Dimension" help="Compression size" />
   </inputs>
   <command>echo "\$PWD"; cp $query ${query.name}; cp $db ${db.name}; (/home/galaxy-bitlab/galaxy/tools/chromeister/bin/CHROMEISTER -query ${query.name} -db ${db.name} -dimension $dimension -out ${query.name}-${db.name}.mat) &amp;>/dev/null ; rm ${query.name}; rm ${db.name}; Rscript /home/galaxy-bitlab/galaxy/tools/chromeister/bin/compute_score.R  ${query.name}-${db.name}.mat $dimension; mv ${query.name}-${db.name}.mat $output; mv ${query.name}-${db.name}.mat.filt.png $outputIMAGEN ; mv ${query.name}-${db.name}.mat.events.txt $outputEVENTS; rm hits-XY-${query.name}-${db.name}.mat.hits</command>
  <outputs>
      <data name="output" format="txt" label="Comparison matrix"/>
      <data name="outputIMAGEN" format="png" label="Comparison dotplot"/>
      <data name="outputEVENTS" format="txt" label="Detected events"/>
  </outputs>
</tool>