# HG changeset patch
# User jeremie
# Date 1404308786 14400
# Node ID 44d381ebe8a5eedbd17adbb54091714b27a63efd
# Parent  7cd61ef578b5d653c2c2c2840e2e3601ec4e9e23
Uploaded

diff -r 7cd61ef578b5 -r 44d381ebe8a5 breakdancer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/breakdancer.xml	Wed Jul 02 09:46:26 2014 -0400
@@ -0,0 +1,90 @@
+<tool id="breakdancer" name="breakdancer" version="1.4.4">
+	<requirements>
+		<requirement type="package" version="1.4.4">breakdancer</requirement>
+	</requirements>
+
+	<description>
+		BreakDancer, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.  BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs.  Please read our paper for detailed algorithmic description. http://www.nature.com/nmeth/journal/v6/n9/abs/nmeth.1363.html
+
+		The input is a set of map files produced by a front-end aligner such as MAQ, BWA, NovoAlign and Bfast
+
+		The output format
+		----------------------
+		BreakDancer's output file consists of the following columns:
+
+		1. Chromosome 1
+		2. Position 1
+		3. Orientation 1
+		4. Chromosome 2
+		5. Position 2
+		6. Orientation 2
+		7. Type of a SV
+		8. Size of a SV
+		9. Confidence Score
+		10. Total number of supporting read pairs
+		11. Total number of supporting read pairs from each map file
+		12. Estimated allele frequency
+		13. Software version
+		14. The run parameters
+	</description>
+
+	<parallelism method="basic"></parallelism>
+
+	<command interpreter="python">
+		breakdancer.py
+		<!-- required -->
+		-i1 $inputBamFile
+		-o1 $outputRawFile
+		<!-- optional -->
+		-o2 $outputVcfFile
+		-o $chromosome
+		-s $minLength
+		-c $cutoff
+		-m $maxSvSize
+		-q $minMapQuality
+		-r $minReadDepth
+		-x $maxHaploidCov
+		-b $bufferSize
+	#if $onlyTrans:
+		-t
+	#end if
+		-d $prefix
+	#if $bedFormat:
+		-g
+	#end if
+		<!-- -l
+		-a
+		-h
+		-y -->
+<!-- parser.add_argument('-l', dest='matePair', required=False, help='analyze Illumina long insert (mate-pair) library')
+# parser.add_argument('-a', dest='sortByLibrary', action='store_true', help='print out copy number and support reads per library rather than per bam', default=False)
+# parser.add_argument('-h', dest='', action='store_true', help='print out Allele Frequency column', default=False)
+parser.add_argument('-y', dest='scoreFilter', type=int, required=False, help='output score filter', default=30) -->
+
+	</command>
+	
+	<inputs>
+		<param name="inputBamFile" format="bam" type="data" label="input bam file" />
+		<!-- optional -->
+		<param name="chromosome" type="text" label="operate on a single chromosome" value="" />
+		<param name="chromosome" type="integer" label="minimum length of a region" value="7" />
+		<param name="cutoff" type="integer" label="cutoff in unit of standard deviation" value="3" />
+		<param name="maxSvSize" type="integer" label="maximum SV size" value="1000000000" />
+		<param name="minMapQuality" type="integer" label="minimum alternative mapping quality" value="35" />
+		<param name="minReadDepth" type="integer" label="minimum number of read pairs required to establish a connection" value="2" />
+		<param name="maxHaploidCov" type="integer" label="maximum threshold of haploid sequence coverage for regions to be ignored" value="1000" />
+		<param name="bufferSize" type="integer" label="buffer size for building connection" value="100" />
+		<param name="onlyTrans" type="boolean" label="only detect transchromosomal rearrangement" checked="False" />
+		<param name="bufferSize" type="text" label="prefix of fastq files that SV supporting reads will be saved by library" value="" />
+		<param name="bedFormat" type="boolean" label="dump SVs and supporting reads in BED format for GBrowse" checked="False" />
+	</inputs>
+
+	<outputs>
+		<data name="outputRawFile" format="tabular" />
+		<data name="outputVcfFile" format="vcf" />
+	</outputs>
+
+	<help>
+	help
+	</help>
+</tool>
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