Mercurial > repos > malbuquerque > factera
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author | malbuquerque |
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date | Fri, 16 Jan 2015 20:15:33 -0500 |
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<tool id="factera" name="FACTERA" version="1.4.3"> <description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="2.2.26+">blast+</requirement> <requirement type="package" version="310">ucsc_user_apps</requirement> <requirement type="package" version="5.18.1">perl</requirement> <requirement type="package" version="1.4.3">factera</requirement> <requirement type="package" version="3.0608">perl_descriptive_statistics</requirement> <requirement type="set_environment">FACTERA_DIR</requirement> </requirements> <command> <!-- Run commands using Galaxy perl --> ln -s $sortedBam ./input.bam; ln -s $sortedBam.metadata.bam_index ./input.bam.bai; #if $cond.additionalOpt == "no" perl \$FACTERA_DIR/factera-v1.4.3.pl -F -o ./ input.bam $exonBed $genome2Bit; #else perl \$FACTERA_DIR/factera-v1.4.3.pl -F -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 ./ input.bam $exonBed $genome2Bit; #end if <!-- Keep only the fusion file --> if [ -e *fusions.txt ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi </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="twobit" 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>