# HG changeset patch
# User erasmus-medical-center
# Date 1493366168 14400
# Node ID 173ca9768e22ef6a47427452f34b62ddf3188a08
# Parent  9495360713d4f6b31768b09b7114fe8a3dbe566c
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit d29f5735b74a3919e6fc16c10435867ed4450576

diff -r 9495360713d4 -r 173ca9768e22 dr-disco_bam-extract.xml
--- a/dr-disco_bam-extract.xml	Thu Mar 16 04:24:23 2017 -0400
+++ b/dr-disco_bam-extract.xml	Fri Apr 28 03:56:08 2017 -0400
@@ -40,12 +40,15 @@
         </test>
     </tests>
     
-    <help>
-Extract reads from two chromosomal positions (and also takes mates with the same name)
+    <help><![CDATA[
+
+**What it does**
+
+Extract reads that have their mate within one of two chromosomal positions (and also takes mates that correspond to these reads)
 
 Regions are in the format:
    chr1:123-546
-    </help>
+    ]]></help>
     
      <expand macro="citations"/>
 </tool>
diff -r 9495360713d4 -r 173ca9768e22 dr-disco_detect.xml
--- a/dr-disco_detect.xml	Thu Mar 16 04:24:23 2017 -0400
+++ b/dr-disco_detect.xml	Fri Apr 28 03:56:08 2017 -0400
@@ -34,7 +34,17 @@
     </tests>
     
     <help><![CDATA[
-        detects
+
+**What it does**
+
+Detects junctions in ('dr-disco fix' prepared) Chimeric alignments and tries to reconstruct fusion genes and genomic breakpoints using a Graph data structure.
+
+This software is in particular designed for RNA-Seq data prepared with random hexamer priming because of the presence of intronic reads.
+
+**Attributions**
+
+This work is part of Youri Hoogstrate's PhD thesis.
+
     ]]></help>
     
      <expand macro="citations"/>
diff -r 9495360713d4 -r 173ca9768e22 dr-disco_fix.xml
--- a/dr-disco_fix.xml	Thu Mar 16 04:24:23 2017 -0400
+++ b/dr-disco_fix.xml	Fri Apr 28 03:56:08 2017 -0400
@@ -29,7 +29,7 @@
 
 **What it does**
 
-Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (extract) and for visualization in genome browsers.
+Dr. Disco fix prepares chimeric alignment files produced by STAR for analysis with Dr. Disco (detect) and for visualization in genome browsers.
 
     ]]></help>
      <expand macro="citations"/>
diff -r 9495360713d4 -r 173ca9768e22 macros.xml
--- a/macros.xml	Thu Mar 16 04:24:23 2017 -0400
+++ b/macros.xml	Fri Apr 28 03:56:08 2017 -0400
@@ -1,12 +1,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.3.4">dr-disco</requirement>
+            <requirement type="package" version="0.6.0">dr-disco</requirement>
             <yield/>
         </requirements>
     </xml>
     
-    <token name="@TOOL_VERSION@">0.3.4</token>
+    <token name="@TOOL_VERSION@">0.6.0</token>
 
     <xml name="version_command">
         <version_command>dr-disco --version | head -n 1</version_command>
diff -r 9495360713d4 -r 173ca9768e22 test-data/detect.txt
--- a/test-data/detect.txt	Thu Mar 16 04:24:23 2017 -0400
+++ b/test-data/detect.txt	Fri Apr 28 03:56:08 2017 -0400
@@ -1,2 +1,2 @@
-chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	filter-status	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	data-structure
-chr21	39877811	-	chr21	42873374	+	n_discordant_reads=0<1,n_support=3<8	intronic	9	6	3	0	1	1	1	0	0	1.0	1.0	chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3)
+chr-A	pos-A	direction-A	chr-B	pos-B	direction-B	genomic-distance	filter-status	circRNA	intronic/exonic	score	soft+hardclips	n-split-reads	n-discordant-reads	n-edges	n-nodes-A	n-nodes-B	n-splice-junc-A	n-splice-junc-B	entropy-bp-edge	entropy-all-edges	bp-pos-stddev	entropy-disco-bps	data-structure
+chr21	39877811	-	chr21	42873374	+	2995563	n_discordant_reads=0<1,n_support=3<8	linear	intronic	9	6	3	0	1	1	1	0	0	1.0000	1.0000	0.0000	0.0000	chr21:39877811/39877812(-)->chr21:42873374/42873375(+):(spanning_paired_1_t:3,spanning_paired_2_t:3)
diff -r 9495360713d4 -r 173ca9768e22 test-data/fix_test-01.fixed.bam
Binary file test-data/fix_test-01.fixed.bam has changed