# HG changeset patch
# User erasmus-medical-center
# Date 1489652663 14400
# Node ID 9495360713d4f6b31768b09b7114fe8a3dbe566c
# Parent  fca9c1ace23c011bd11ea89c4bc61ee58bc55a1f
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b

diff -r fca9c1ace23c -r 9495360713d4 dr-disco_bam-extract.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dr-disco_bam-extract.xml	Thu Mar 16 04:24:23 2017 -0400
@@ -0,0 +1,51 @@
+<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0">
+    <description>Extracts reads from two targeted regions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements" />
+    <expand macro="version_command"/>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        dr-disco bam-extract
+            '$region1'
+            '$region2'
+            '$output'
+            '$input_alignment'
+    ]]></command>
+    <inputs>
+        <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" />
+        <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" />
+        <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_alignment" value="bam_extract.bam" />
+            <param name="region1" value="chr21:39737183-40035618" />
+            <param name="region2" value="chr21:42834478-42882085" />
+            
+            <output name="output" file="bam_extract.bam" />
+        </test>
+        <test>
+            <param name="input_alignment" value="bam_extract.bam" />
+            <param name="region1" value="chr22:39737183-40035618" />
+            <param name="region2" value="chr11:42834478-42882085" />
+            
+            <output name="output" file="bam_extract.empty.bam" />
+        </test>
+    </tests>
+    
+    <help>
+Extract reads from two chromosomal positions (and also takes mates with the same name)
+
+Regions are in the format:
+   chr1:123-546
+    </help>
+    
+     <expand macro="citations"/>
+</tool>
diff -r fca9c1ace23c -r 9495360713d4 dr-disco_bam_extract.xml
--- a/dr-disco_bam_extract.xml	Wed Jan 25 08:06:06 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@-g0">
-    <description>Extracts reads from two targeted regions</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    
-    <expand macro="requirements" />
-    <expand macro="version_command"/>
-    
-    <command><![CDATA[
-        dr-disco bam-extract
-            '$region1'
-            '$region2'
-            '$output'
-            '$input_alignment'
-    ]]></command>
-    <inputs>
-        <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" />
-        <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" />
-        <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
-    </inputs>
-    <outputs>
-        <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
-    </outputs>
-    
-    <tests>
-        <test>
-            <param name="input_alignment" value="bam_extract.bam" />
-            <param name="region1" value="chr21:39737183-40035618" />
-            <param name="region2" value="chr21:42834478-42882085" />
-            
-            <output name="output" file="bam_extract.bam" />
-        </test>
-        <test>
-            <param name="input_alignment" value="bam_extract.bam" />
-            <param name="region1" value="chr22:39737183-40035618" />
-            <param name="region2" value="chr11:42834478-42882085" />
-            
-            <output name="output" file="bam_extract.empty.bam" />
-        </test>
-    </tests>
-    
-    <help>
-Extract reads from two chromosomal positions (and also takes mates with the same name)
-
-Regions are in the format:
-   chr1:123-546
-    </help>
-    
-     <expand macro="citations"/>
-</tool>
diff -r fca9c1ace23c -r 9495360713d4 dr-disco_detect.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dr-disco_detect.xml	Thu Mar 16 04:24:23 2017 -0400
@@ -0,0 +1,41 @@
+<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
+    <description>Detects break-points in RNA-seq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        dr-disco
+            detect
+                --min-e-score '${min_e_score}'
+                '${table_fusion_events}'
+                '${star_discordant_alignment_fixed}'
+    ]]></command>
+    <inputs>
+        <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>
+    
+    <outputs>
+        <data name="table_fusion_events" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="star_discordant_alignment_fixed" value="detect.bam" />
+            <param name="min_e_score" value="8" />
+
+            <output name="table_fusion_events" file="detect.txt" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+        detects
+    ]]></help>
+    
+     <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r fca9c1ace23c -r 9495360713d4 dr-disco_fix.xml
--- a/dr-disco_fix.xml	Wed Jan 25 08:06:06 2017 -0500
+++ b/dr-disco_fix.xml	Thu Mar 16 04:24:23 2017 -0400
@@ -1,26 +1,36 @@
 <tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
-    <description>Fixes and annotates chimeric alignments</description>
+    <description>Fixes chimeric alignments from STAR</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    
+
     <expand macro="requirements" />
     <expand macro="version_command" />
-    
-    <command><![CDATA[
-        dr-disco fix '${output}' '${star_discordant_alignment}'
+
+    <command detect_errors="exit_code"><![CDATA[
+        dr-disco fix '${alignment_fixed}' '${star_discordant_alignment}'
     ]]></command>
     <inputs>
         <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
     </inputs>
     <outputs>
-        <data name="output" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
+        <data name="alignment_fixed" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
     </outputs>
+
     <tests>
+        <test>
+            <param name="star_discordant_alignment" value="fix_test-01.bam"/>
+
+            <output name="alignment_fixed" file="fix_test-01.fixed.bam" />
+        </test>
     </tests>
     
-    <help>
-    </help>
-    
+    <help><![CDATA[
+
+**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.
+
+    ]]></help>
      <expand macro="citations"/>
 </tool>
\ No newline at end of file
diff -r fca9c1ace23c -r 9495360713d4 dr-disco_intronic.xml
--- a/dr-disco_intronic.xml	Wed Jan 25 08:06:06 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
-    <description>Detects break-points in RNA-seq</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    
-    <expand macro="requirements"/>
-    <expand macro="version_command"/>
-    
-    <command><![CDATA[
-        ## old thing that evolved as such - depending on what the future will bring leave it out or include it...
-        touch empty.txt &&
-        
-        dr-disco
-            intronic
-                -m '${min_e_score}'
-                '${output}'
-                empty.txt
-                '${star_discordant_alignment_fixed}'
-    ]]></command>
-    <inputs>
-        <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
-        <param name="min_e_score" type="integer" value="8" min="0"
-            label="Minimal score to initiate pulling sub-graphs"
-            help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." />
-    </inputs>
-    
-    <outputs>
-        <data name="output" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" />
-    </outputs>
-    
-    <tests>
-    </tests>
-    
-    <help>
-    </help>
-    
-     <expand macro="citations"/>
-</tool>
\ No newline at end of file
diff -r fca9c1ace23c -r 9495360713d4 macros.xml
--- a/macros.xml	Wed Jan 25 08:06:06 2017 -0500
+++ b/macros.xml	Thu Mar 16 04:24:23 2017 -0400
@@ -1,12 +1,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.2.0">dr-disco</requirement>
+            <requirement type="package" version="0.3.4">dr-disco</requirement>
             <yield/>
         </requirements>
     </xml>
     
-    <token name="@TOOL_VERSION@">0.2.0</token>
+    <token name="@TOOL_VERSION@">0.3.4</token>
 
     <xml name="version_command">
         <version_command>dr-disco --version | head -n 1</version_command>
@@ -15,13 +15,13 @@
     <xml name="citations">
         <citations>
             <!--<citation type="doi"></citation>-->
-        <citation type="bibtex">
-           @unpublished{dr_disco,
-              author = {Youri Hoogstrate},
-              title  = {Dr. Disco: detecting genomic breakpoints of TMPRSS2-ERG in prostate cancer using RNA-Seq data only},
-              url    = {https://github.com/yhoogstrate/dr-disco}
-            }
-        </citation>
+            <citation type="bibtex">
+               @unpublished{dr_disco,
+                  author = {Youri Hoogstrate},
+                  title  = {Dr. Disco: detecting genomic breakpoints of TMPRSS2-ERG in prostate cancer using RNA-Seq data only},
+                  url    = {https://github.com/yhoogstrate/dr-disco}
+                }
+            </citation>
             <yield />
         </citations>
     </xml>
diff -r fca9c1ace23c -r 9495360713d4 test-data/detect.bam
Binary file test-data/detect.bam has changed
diff -r fca9c1ace23c -r 9495360713d4 test-data/detect.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/detect.txt	Thu Mar 16 04:24:23 2017 -0400
@@ -0,0 +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)
diff -r fca9c1ace23c -r 9495360713d4 test-data/fix_test-01.bam
Binary file test-data/fix_test-01.bam has changed
diff -r fca9c1ace23c -r 9495360713d4 test-data/fix_test-01.fixed.bam
Binary file test-data/fix_test-01.fixed.bam has changed