# HG changeset patch
# User jeremie
# Date 1403004866 14400
# Node ID 6fda22b6c486eae1e1339545d3fe33a500e6b2af
# Parent  ba6d471d43ad0f45f9827f4b675040d56b428cb4
Uploaded

diff -r ba6d471d43ad -r 6fda22b6c486 delly.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/delly.xml	Tue Jun 17 07:34:26 2014 -0400
@@ -0,0 +1,77 @@
+<tool id="delly" name="delly" version="">
+	<description>structural variant prediction method</description>
+	<parallelism method="basic"></parallelism>
+
+	<command interpreter="python">
+		delly.py
+		-b $bam
+		-t
+		#if $checkDel:
+			DEL
+		#end if
+		#if $checkDup:
+			DUP
+		#end if
+		#if $checkInv:
+			INV
+		#end if
+		#if $checkTra:
+			TRA
+		#end if
+		-q $map_qual
+		-s $mad_cutoff
+		-g $genome
+		-m $min_flank
+		-e $epsilon
+		-o $output
+	</command>
+
+	<inputs>
+		<param format="bam" name="bam" type="data" label="bam file" help="" />
+		<param name="checkDel" type="boolean" label="Check Deletion?" checked="true"/>
+		<param name="checkDup" type="boolean" label="Check Duplication?" checked="true"/>
+		<param name="checkInv" type="boolean" label="Check Inversion?" checked="true"/>
+		<param name="checkTra" type="boolean" label="Check Translation?" checked="true"/>
+		<param name="map_qual" type="integer" label="min. paired-end mapping quality" value="0" />
+		<param name="mad_cutoff" type="integer" label="insert size cutoff, median+s*MAD (deletions only)" value="5" />
+		<param name="min_flank" type="integer" label="minimum flanking sequence size" value="13" />
+		<param name="epsilon" type="float" label="allowed epsilon deviation of PE vs. SR deletion" value="0.1" />
+		<param name="genome" type="text" label="genome" value="null" />
+	</inputs>
+
+	<outputs>
+		<data format="vcf" name="output" label="VCF output of delly" />
+	</outputs>
+
+	<help>
+DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
+It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.
+
+DELLY (Version: 0.5.5)
+Contact: Tobias Rausch (rausch@embl.de)
+
+Generic options:
+  -? [ --help ]                    show help message
+  -t [ --type ] arg (=DEL)         SV analysis type (DEL, DUP, INV, TRA)
+  -o [ --outfile ] arg (="sv.vcf") SV output file
+  -x [ --exclude ] arg (="")       file with chr to exclude
+
+PE options:
+  -q [ --map-qual ] arg (=0)   min. paired-end mapping quality
+  -s [ --mad-cutoff ] arg (=5) insert size cutoff, median+s*MAD (deletions only)
+
+SR options:
+  -g [ --genome ] arg          genome fasta file
+  -m [ --min-flank ] arg (=13) minimum flanking sequence size
+
+Genotyping options:
+  -v [ --vcfgeno ] arg (="site.vcf") input vcf file for genotyping only
+  -u [ --geno-qual ] arg (=20)       min. mapping quality for genotyping
+	</help>
+
+	<tests>
+		<test>
+		</test>
+	</tests>
+
+</tool>
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