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comparison chromeister/chromeister.xml @ 3:0589a1c5f33a draft default tip

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Fixed absolute paths
author bitlab
date Mon, 07 Oct 2019 08:43:57 -0400
parents 5ce7e50f159b
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2:5ce7e50f159b 3:0589a1c5f33a
5 <param name="db" type="data" format="fasta" label="Reference sequence" help="Reference 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" /> 6 <param name="dimension" type="integer" value="1000" label="Dimension" help="Compression size" />
7 <param name="kmer" type="integer" value="32" label="Kmer" help="Seed size used to find unique hits" /> 7 <param name="kmer" type="integer" value="32" label="Kmer" help="Seed size used to find unique hits" />
8 <param name="diffuse" type="integer" value="4" label="Difusse value" help="Level of the heuristic subsampling employed" /> 8 <param name="diffuse" type="integer" value="4" label="Difusse value" help="Level of the heuristic subsampling employed" />
9 </inputs> 9 </inputs>
10 <command>cp $query "${query.name}"; cp $db "${db.name}"; (/home/galaxy-bitlab/galaxy/tools/chromeister/bin/CHROMEISTER -query "${query.name}" -db "${db.name}" -dimension $dimension -kmer $kmer -diffuse $diffuse -out "${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> 10 <command>make all -C ${__tool_directory__}/src ; cp $query "${query.name}"; cp $db "${db.name}"; (${__tool_directory__}/bin/CHROMEISTER -query "${query.name}" -db "${db.name}" -dimension $dimension -kmer $kmer -diffuse $diffuse -out "${query.name}"-"${db.name}".mat) &amp;>/dev/null ; rm "${query.name}"; rm "${db.name}"; Rscript ${__tool_directory__}/bin/compute_score.R "${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>
11 <outputs> 11 <outputs>
12 <data name="output" format="txt" label="Comparison matrix"/> 12 <data name="output" format="txt" label="Comparison matrix"/>
13 <data name="outputIMAGEN" format="png" label="Comparison dotplot"/> 13 <data name="outputIMAGEN" format="png" label="Comparison dotplot"/>
14 <data name="outputEVENTS" format="txt" label="Detected events"/> 14 <data name="outputEVENTS" format="txt" label="Detected events"/>
15 </outputs> 15 </outputs>