diff dr-disco_bam-extract.xml @ 1:9495360713d4 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 6ca895dfcaa94693a54a90716d669d9488bee45b

--- /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>