comparison chromeister/chromeister.xml @ 1:3d1fbde7e0cc draft default tip

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author alvarofaure
date Thu, 13 Dec 2018 03:41:58 -0500
parents 7fdf47a0bae8
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0:7fdf47a0bae8 1:3d1fbde7e0cc
1 <tool id="chromeister" name="Chromeister">
2 <description>A heuristic approach for ultra fast previsualization of pairwise genome comparisons</description>
3 <inputs>
4 <param name="query" type="data" format="fasta" label="Query sequence" help="Query sequence file in fasta format" />
5 <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference sequence file in fasta format" />
6 <param name="dimension" type="integer" value="1000" label="Dimension" help="Compression size" />
7 </inputs>
8 <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>
9 <outputs>
10 <data name="output" format="txt" label="Comparison matrix"/>
11 <data name="outputIMAGEN" format="png" label="Comparison dotplot"/>
12 <data name="outputEVENTS" format="txt" label="Detected events"/>
13 </outputs>
14 </tool>