# HG changeset patch
# User iuc
# Date 1638007390 0
# Node ID 2ed961caae0a16643dd0d3f3c9ba1fa0dff16588

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"

diff -r 000000000000 -r 2ed961caae0a bamtools_split_mapped.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools_split_mapped.xml	Sat Nov 27 10:03:10 2021 +0000
@@ -0,0 +1,56 @@
+<tool id="bamtools_split_mapped" name="Split BAM by Mapped" 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 -mapped
+            -in localbam.bam
+            -stub split_bam
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by mapped/unmapped"/>
+    </inputs>
+    <outputs>
+        <data format="bam" name="mapped" label="${input_bam.name} mapped" from_work_dir="split_bam.MAPPED.bam" />
+        <data format="bam" name="unmapped" label="${input_bam.name} unmapped" from_work_dir="split_bam.UNMAPPED.bam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
+            <output name="mapped" file="split_bam.MAPPED.bam"  compare="sim_size" delta="200" />
+            <output name="unmapped" file="split_bam.UNMAPPED.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 (MAPPED) and (UNMAPPED) containing mapped and unmapped 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>
diff -r 000000000000 -r 2ed961caae0a macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Nov 27 10:03:10 2021 +0000
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">2.5.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">bamtools</requirement>
+            <requirement type="package" version="1.4.1">samtools</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btr174</citation>
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
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diff -r 000000000000 -r 2ed961caae0a test-data/split_bam.UNMAPPED.bam
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