Mercurial > repos > malbuquerque > delly
view delly.xml @ 25:77df0ec10965 draft
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author | malbuquerque |
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date | Tue, 20 Jan 2015 18:47:26 -0500 |
parents | 226f241f0c92 |
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<tool id="delly" name="DELLY" version="0.6.1"> <description>structural variant discovery by integrated paired-end and split-read analysis</description> <requirements> <requirement type="package" version="0.6.1">delly</requirement> <requirement type="set_environment">DELLY_DIR</requirement> </requirements> <command> <!-- BAM and BAI linking, (1) link BAM to new BAM file & (2) link BAM metadata to new BAI file --> #for $i, $s in enumerate( $repeatBam ) ln -s $s.sortedBam ./input$(i).bam; ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai; #end for <!-- Sets args to a list of types selected --> #if not isinstance( $type.value, list ): #set $args = [ $type.value ] #else: #set $args = $type.value #end if <!-- Run Delly Jobs for each type selected --> #for $option in $args <!-- NEED TO FIX --> <!-- Delly should be automatically installed into the galaxy instance and should not be running off the computers specific tool set --> \$DELLY_DIR/src/delly -t $option -o ./output.$(option).vcf -q $mapQual -s $madCutoff #if $option == "DEL" -m $minFlank #end if -u $genoQual -v $vcfgeno -g $genome <!-- add each input bam to command --> #for $i, $s in enumerate( $repeatBam ) ./input$(i).bam #end for ; #end for <!-- Combine VCF Files and Sort Lexographically --> #set $option = $args[0] grep ^\# output.$(option).vcf > $outfile; grep ^\# -v output.$(option).vcf > variants.txt; <!-- If we called more than a single variant type, concatenate all the other types variant output --> #if isinstance( $type.value, list ): #for $option in $args[1:] grep ^\# -v output.$(option).vcf >> variants.txt; #end for #end if <!-- Sort all variant output, assuming that it will sort lexographically by chromosome, then position, ID --> <!-- In future, maybe develop a script to sort by bam header --> sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt; <!-- Filter Variants that have Passed Quality Checks --> #if $filterCalls awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile; #else cat sortedVariants.txt >> $outfile; #end if </command> <inputs> <!-- General Options --> <param name="type" type="select" multiple="true" display="checkboxes" label="Variant Types"> <option value="DEL" selected="true">Deletions</option> <option value="DUP" selected="true">Tandem Duplications</option> <option value="INV" selected="true">Inversions</option> <option value="TRA" selected="true">Translocations</option> </param> <repeat name="repeatBam" title="Bam Alignment" min="1" default="1" > <param format="bam" name="sortedBam" type="data" label="File" /> </repeat> <param name="excludeFile" type="data" optional="true" label="Chromosomes to Exclude"/> <param name="filterCalls" type="boolean" value="false" label="Filter Poor Variant Calls"/> <!-- Paired End Options --> <param name="mapQual" type="integer" value="0" min="0" max="255" label="PE - Minimum Mapping Quality" /> <param name="madCutoff" type="integer" value="9" min="0" max="255" label="PE - Insert Size Cutoff" /> <!-- SR Options --> <param format="fasta" name="genome" type="data" optional="true" label="SR - Genome Fasta File" /> <param name="minFlank" type="integer" value="13" label="SR - Minimum Flanking Sequence" /> <!-- Genotyping Options --> <param format="vcf" name="vcfgeno" type="data" optional="true" label="GT - Input VCF" /> <param name="genoQual" type="integer" value="20" min="0" max="255" label="GT - Minimum Mapping Quality" /> </inputs> <outputs> <data format="vcf" name="outfile" /> </outputs> <help> </help> </tool>