# HG changeset patch
# User erasmus-medical-center
# Date 1485349566 18000
# Node ID fca9c1ace23c011bd11ea89c4bc61ee58bc55a1f

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit a6e0161a14202e3fc166b3cf8ecbafed54ec403a

diff -r 000000000000 -r fca9c1ace23c dr-disco_bam_extract.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dr-disco_bam_extract.xml	Wed Jan 25 08:06:06 2017 -0500
@@ -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><![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 ${input_alignment.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_alignment" value="bam_extract.bam" />
+            <param name="region1" value="chr21:39737183-40035618" />
+            <param name="region2" value="chr21:42834478-42882085" />
+            
+            <output name="output" file="bam_extract.bam" />
+        </test>
+        <test>
+            <param name="input_alignment" value="bam_extract.bam" />
+            <param name="region1" value="chr22:39737183-40035618" />
+            <param name="region2" value="chr11:42834478-42882085" />
+            
+            <output name="output" file="bam_extract.empty.bam" />
+        </test>
+    </tests>
+    
+    <help>
+Extract reads from two chromosomal positions (and also takes mates with the same name)
+
+Regions are in the format:
+   chr1:123-546
+    </help>
+    
+     <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r fca9c1ace23c dr-disco_fix.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dr-disco_fix.xml	Wed Jan 25 08:06:06 2017 -0500
@@ -0,0 +1,26 @@
+<tool id="dr_disco_fix" name="Dr. Disco (fix)" version="@TOOL_VERSION@-g0">
+    <description>Fixes and annotates chimeric alignments</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    
+    <command><![CDATA[
+        dr-disco fix '${output}' '${star_discordant_alignment}'
+    ]]></command>
+    <inputs>
+        <param name="star_discordant_alignment" type="data" format="bam" label="Discordant alignment file of STAR" />
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} on ${star_discordant_alignment}" />
+    </outputs>
+    <tests>
+    </tests>
+    
+    <help>
+    </help>
+    
+     <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r fca9c1ace23c dr-disco_intronic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dr-disco_intronic.xml	Wed Jan 25 08:06:06 2017 -0500
@@ -0,0 +1,39 @@
+<tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0">
+    <description>Detects break-points in RNA-seq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    
+    <command><![CDATA[
+        ## old thing that evolved as such - depending on what the future will bring leave it out or include it...
+        touch empty.txt &&
+        
+        dr-disco
+            intronic
+                -m '${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 000000000000 -r fca9c1ace23c macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jan 25 08:06:06 2017 -0500
@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="0.2.0">dr-disco</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    
+    <token name="@TOOL_VERSION@">0.2.0</token>
+
+    <xml name="version_command">
+        <version_command>dr-disco --version | head -n 1</version_command>
+    </xml>
+
+    <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>
+            <yield />
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r fca9c1ace23c test-data/bam_extract.bam
Binary file test-data/bam_extract.bam has changed
diff -r 000000000000 -r fca9c1ace23c test-data/bam_extract.empty.bam
Binary file test-data/bam_extract.empty.bam has changed