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BAM_preprocessingPairs.xml |
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| diff -r 35fb765cd586 -r 89b207100214 BAM_preprocessingPairs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BAM_preprocessingPairs.xml Mon Jun 11 12:29:57 2012 -0400 |
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| @@ -0,0 +1,77 @@ +<tool id="svdetect_preprocessing" name="BAM preprocessing"> + + <description>to get abnormal pairs</description> + + <command interpreter="perl"> BAM_preprocessingPairs.pl -t '$readType' -p '$pairType' -n '$nbrePair' -s '$isizeMin' -S '$isizeMax' -f '$foldPair' -o $__new_file_path__/svdetect -b '$abBAM' -l '$log' -N $sample_name + #if $newBam.pairNormal=="yes" + -d -x '$normBAM' + #end if + '$inputBam' + </command> + + <inputs> + <param name="sample_name" type="text" value="sample" label="Sample Name"/> + <param name="inputBam" type="data" format="bam" label="BAM input file"/> + <param name="readType" type="select" label="Read type"> + <option value="1">Illumina</option> + <option value="0">SOLiD</option> + </param> + <param name="pairType" type="select" label="Library type"> + <option value="1">Paired-end</option> + <option value="0">Mate-Pair</option> + </param> + <conditional name="newBam"> + <param name="pairNormal" type="select" label="Do you want an additional bam file listing concordant mapped pairs?" help="Dump normal pairs into a file sample_name.norm.bam/sam"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <!-- do nothing here --> + </when> + <when value="no"> + <!-- do nothing here --> + </when> + </conditional> + <param name="nbrePair" value="1000000" type="integer" size="30" label="Number of pairs for calculating mu (µ) and sigma (σ) lengths"/> + <param name="isizeMin" value="0" type="integer" size="30" label="Minimum value of ISIZE for calculating mu (µ) and sigma (σ) lengths"/> + <param name="isizeMax" value="10000" type="integer" size="30" label="Maximum value of ISIZE for calculating mu (µ)and sigma( σ) lengths"/> + <param name="foldPair" value="3" type="float" size="30" label="Minimal number of sigma (σ) fold for filtering pairs"/> + </inputs> + + <outputs> + <data format="bam" name="abBAM" label="${$sample_name}.ab.bam"/> + <data format="txt" name="log" label="${$sample_name}.svdetect_preprocessing.log"/> + <data format="bam" name="normBAM" label="${$sample_name}.norm.bam"> + <filter>newBam['pairNormal'] == 'yes'</filter> + </data> + </outputs> + + <help> + +**What it does** + +Bam_preprocessingPairs - Version 0.4b + +Preprocessing of mates to get anomalously mapped mate-pair/paired-end reads as input for SVDetect. + +From all pairs mapped onto the reference genome, this script outputs abnormal pairs: + + * mapped on two different chromosomes + * with an incorrect strand orientation and/or pair order + * with an insert size distance +- sigma threshold + +into a file prefix.ab.bam/sam sorted by read names + +-BAM/SAM File input format only. + +SAMtools required for BAM files + +----- + +.. class:: infomark + +Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect. + + </help> + +</tool> |