# HG changeset patch
# User erasmus-medical-center
# Date 1505392512 14400
# Node ID 922b52cf9b358052b6140dd250af6a84f5541d27
# Parent  6b87499054f683e16fd7c740a2e030a7a78ecbd3
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b4991fb40364a975d0ea782035b930874c57665c

diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_bam-extract.xml
--- a/dr-disco_bam-extract.xml	Thu Sep 14 06:24:47 2017 -0400
+++ b/dr-disco_bam-extract.xml	Thu Sep 14 08:35:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0">
+<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@">
     <description>Extracts reads from two targeted regions</description>
 
     <macros>
diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_classify.xml
--- a/dr-disco_classify.xml	Thu Sep 14 06:24:47 2017 -0400
+++ b/dr-disco_classify.xml	Thu Sep 14 08:35:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@-g0">
+<tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@">
     <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description>
 
     <macros>
diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_detect.xml
--- a/dr-disco_detect.xml	Thu Sep 14 06:24:47 2017 -0400
+++ b/dr-disco_detect.xml	Thu Sep 14 08:35:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@-g0">
+<tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@">
     <description>Detects break-points in RNA-seq</description>
     <macros>
         <import>macros.xml</import>
@@ -15,7 +15,7 @@
                 '${output_fusion_events}'
     ]]></command>
     <inputs>
-        <param name="star_discordant_alignment_fixed" type="data" format="tabular" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
+        <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
         <param name="min_e_score" argument="--min-e-score" type="integer" value="8" min="0"
                label="Minimal score to initiate pulling sub-graphs" help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." />
     </inputs>
diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_fix.xml
--- a/dr-disco_fix.xml	Thu Sep 14 06:24:47 2017 -0400
+++ b/dr-disco_fix.xml	Thu Sep 14 08:35:12 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
+<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@">
     <description>Fixes chimeric alignments from STAR</description>
     <macros>
         <import>macros.xml</import>
diff -r 6b87499054f6 -r 922b52cf9b35 dr-disco_integrate.xml
--- a/dr-disco_integrate.xml	Thu Sep 14 06:24:47 2017 -0400
+++ b/dr-disco_integrate.xml	Thu Sep 14 08:35:12 2017 -0400
@@ -1,9 +1,9 @@
-<tool id="dr_disco_integrate" name="Dr. Disco (integrate)" version="@TOOL_VERSION@-g0">
+<tool id="dr_disco_integrate" name="Dr. Disco (integrate)" version="@TOOL_VERSION@">
     <description>Merges corresponding genomic breaks and exon-to-exon junctions</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    
+
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     
@@ -11,7 +11,7 @@
         dr-disco
             integrate
                 #if $gtf:
-                    --gtf ${gtf}
+                    --gtf '${gtf}'
                 #end if
 
                 '${dr_disco_classify_output}'
diff -r 6b87499054f6 -r 922b52cf9b35 macros.xml
--- a/macros.xml	Thu Sep 14 06:24:47 2017 -0400
+++ b/macros.xml	Thu Sep 14 08:35:12 2017 -0400
@@ -5,8 +5,8 @@
             <yield/>
         </requirements>
     </xml>
-    
-    <token name="@TOOL_VERSION@">0.10.0-g2</token>
+
+    <token name="@TOOL_VERSION@">0.10.0-g3</token>
 
     <xml name="version_command">
         <version_command>dr-disco --version | head -n 1</version_command>