Mercurial > repos > alvarofaure > bitlab
comparison chromeister/chromeister.xml @ 0:7fdf47a0bae8 draft
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| author | alvarofaure |
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| date | Wed, 12 Dec 2018 07:18:40 -0500 |
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| -1:000000000000 | 0:7fdf47a0bae8 |
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| 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) &>/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> |