Mercurial > repos > malbuquerque > factera
view factera/factera.xml @ 2:97973e7ca771 draft
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author | malbuquerque |
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date | Thu, 15 Jan 2015 18:29:32 -0500 |
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<tool id="factera" name="FACTERA"> <description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description> <command> <!-- Run commands using Galaxy perl --> #if $cond.additionalOpt.value == "no" perl $FACTERA_DIR/factera-v1.4.3.pl -o ./ $sortedBam $exonBed $genome2Bit #else perl $FACTERA_DIR/factera-v1.4.3.pl -r $cond.r -m $cond.m -x $cond.x -s $cond.s -f $cond.f -S $cond.S -k $cond.k -c $cond.c -b $cond.b -p $cond.p -a $cond.a -o ./ $sortedBam $exonBed $genome2Bit #end if <!-- Keep only the fusion file --> cat *fusions.txt > $outfile; </command> <inputs> <param format="bam" name="sortedBam" type="data" label="Alignment in BAM format" /> <param format="bed" name="exonBed" type="data" label="Genomic coordinates with gene/exon names in fourth column" /> <param format="2bit" name="genome2Bit" type="data" label="Two bit reference sequence" /> <conditional name="cond"> <param type="select" name="additionalOpt" label="Additional Options"> <option value="yes">Yes</option> <option value="no" selected="True">No</option> </param> <when value="yes"> <!-- Names follow command line flags in factera.pl --> <param type="integer" name="r" label="Minimum number of breakpoint-scanning reads required for output" value="5"/> <param type="integer" name="m" label="Minimum number of discordant reads required for each candidate fusion" value="2"/> <param type="integer" name="x" label="Maximum number of breakpoints to examine for each pair of genomic regions" value="5"/> <param type="integer" name="s" label="Minimum number of reads with the same breakpoint" value="1"/> <param type="float" name="f" min="0" max="1" label="Minimum fraction of read bases required for alignment to fusion template" value=".9"/> <param type="float" name="S" min="0" max="1" label="Minimum similarity required for read to match fusion template" value=".95"/> <param type="integer" name="k" label="K-mer size (number of bases) for fragment comparison" value="10"/> <param type="integer" name="c" label="Minimum size of soft-clipped region to consider" value="16"/> <param type="integer" name="b" label="Number of bases flanking breakpoint for fusion template" value="500"/> <param type="integer" name="p" label="Number of threads for blastn search" value="4"/> <param type="integer" name="a" label="Number of bases flanking breakpoint to provide in output" value="50"/> </when> </conditional> </inputs> <outputs> <data format="tabular" name="outfile" /> </outputs> <help>This tool does Factera</help> </tool>