# HG changeset patch
# User jeremie
# Date 1404309643 14400
# Node ID a8f3dba37a9223b481645e0829e09fa0bbb132b6
# Parent  a6f66f70d16634151b11bfa1531f692e71d04ea7
Uploaded

diff -r a6f66f70d166 -r a8f3dba37a92 breakdancer.xml
--- a/breakdancer.xml	Wed Jul 02 09:46:32 2014 -0400
+++ b/breakdancer.xml	Wed Jul 02 10:00:43 2014 -0400
@@ -3,30 +3,7 @@
 		<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>
+	<description>detection of structural variants</description>
 
 	<parallelism method="basic"></parallelism>
 
@@ -67,7 +44,7 @@
 		<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="minLength" 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" />
@@ -85,6 +62,30 @@
 	</outputs>
 
 	<help>
-	help
+	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
 	</help>
 </tool>
\ No newline at end of file