# HG changeset patch
# User jjohnson
# Date 1497891392 14400
# Node ID a83b275f7c418fbd33992638fc5f8b1dca56e76b

Uploaded

diff -r 000000000000 -r a83b275f7c41 ._bamtools_split_ref.xml
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diff -r 000000000000 -r a83b275f7c41 bamtools_split_ref.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools_split_ref.xml	Mon Jun 19 12:56:32 2017 -0400
@@ -0,0 +1,88 @@
+<tool id="bamtools_split_ref" name="Split BAM by Reference" version="2.4.0">
+    <description>into dataset list collection</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 -reference
+            -in localbam.bam 
+            -stub split_bam 
+            ## Preserve order from metadata in the output collection
+            #import re
+            #set $name = $re.sub('\W','_',$re.sub('\.bam$','',$input_bam.name))
+            #if str($refs) != 'None':
+                #set $ref_list = ' '.join(str($refs).split(","))
+            #else 
+                #set $ref_list = ' '.join([$re.sub('^.*__sq__(.+)__sq__.*$','\\1',n) if n.find('__sq__') >= 0 else n for n in str($input_bam.metadata.reference_names).split(',')])
+            #end if
+            && mkdir -p outputs
+            && (export I=0; 
+              for i in $ref_list; 
+                do I=\$((++I)); SN=`printf "split_bam.REF_%s.bam" "\$i"`; 
+                  if [ -e \$SN ]; then FN=`printf "outputs/split_bam%05d%s.%s.bam" \$((I)) '$name' "\$i"`; mv \$SN \$FN; fi;
+                done)
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM dataset to split by reference"/>
+        <param name="refs" type="select" optional="True" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" >
+            <help><![CDATA[Click and type in the box above to see options. You can select multiple entries. 
+                  If "No options available" is displayed, you need to re-detect metadata on the input dataset.
+            ]]></help>
+            <options>
+                <filter type="data_meta" ref="input_bam" key="reference_names" />
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="output_bams" type="list" label="${input_bam.name} Split List">
+            <discover_datasets pattern="split_bam\d*(?P&lt;designation&gt;.+)\.bam" ext="bam" directory="outputs" visible="false"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" ftype="bam" value="bamtools-input2.bam"/>
+            <output_collection name="output_bams"  type="list">
+                <element name="bamtools_input2.chr1"  file="bamtools_input2.chr1" compare="sim_size" delta="500" />
+            </output_collection>
+        </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
+
+**DANGER: Multiple Outputs**
+
+As described below, splitting a BAM dataset(s) on reference name or a tag value can produce very large numbers of outputs. Read below and know what you are doing.
+
+-----
+
+**How it works**
+
+Split alignments by reference name into a dataset list collection.  The collection will be in the same order as the input BAM references.
+
+In cases of unfinished genomes with very large number of reference sequences (scaffolds) 
+it can generate thousands (if not millions) of output datasets.
+
+
+-----
+
+.. 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>
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diff -r 000000000000 -r a83b275f7c41 test-data/bamtools_input_tags.TAG_XG_N.bam
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diff -r 000000000000 -r a83b275f7c41 test-data/split_bam.UNMAPPED.bam
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