Mercurial > repos > iuc > bamtools_split_ref

diff bamtools_split_paired.xml @ 1:9dbf707bebb0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
author: iuc
date: Wed, 11 Jan 2023 12:03:53 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools_split_paired.xml	Wed Jan 11 12:03:53 2023 +0000
@@ -0,0 +1,57 @@
+<tool id="bamtools_split_paired" name="Split BAM by Paired/Single End" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description></description>
+    <macros>
+          <import>macros.xml</import>
+    </macros>
+    <expand macro="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>