diff bamtools-split-paired.xml @ 0:8c17ddca0eee draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools-split-paired.xml	Mon May 15 16:27:18 2017 -0400
@@ -0,0 +1,56 @@
+<tool id="bamSplitPaired" name="Split BAM by Paired/Single End" version="2.4.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="2.4.0">bamtools</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+            ln -s '${input_bam}' 'localbam.bam' &&
+            ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
+            bamtools split -paired
+            -in localbam.bam 
+            -stub split_bam 
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by single_end/paired_end"/>
+    </inputs>
+    <outputs>
+        <data format="bam" name="single" label="${input_bam.name} mapped" from_work_dir="split_bam.SINGLE_END.bam" />
+        <data format="bam" name="paired" label="${input_bam.name} unmapped" from_work_dir="split_bam.PAIRED_END.bam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" ftype="bam" value="bamtools-input-paired.bam"/>
+            <output name="single" file="split_bam.SINGLE_END.bam"  compare="sim_size" delta="200" />
+            <output name="paired" file="split_bam.PAIRED_END.bam"  compare="sim_size" delta="200" />
+        </test>
+    </tests>
+    <help>
+**What is does**
+
+BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
+
+-----
+
+.. class:: warningmark
+
+
+**How it works**
+
+
+Splits the input BAM file into 2 output files named (SINGLE_END) and (PAIRED_END) containing single_end and paired_end reads, respectively.
+
+-----
+
+.. class:: infomark
+
+**More information**
+
+Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
+
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr174</citation>
+    </citations>
+</tool>