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comparison bamtools-split.xml @ 0:8c17ddca0eee draft

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author jjohnson
date Mon, 15 May 2017 16:27:18 -0400
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1 <tool id="bamSplit" name="Split" version="2.4.0">
2 <description>BAM datasets on variety of attributes</description>
3 <requirements>
4 <requirement type="package" version="2.4.0">bamtools</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 echo "BAM" > $report &&
9 #for $bam_count, $input_bam in enumerate( $input_bams ):
10 ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
11 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
12 #end for
13 bamtools
14 split
15 #if str ( $analysis_type.analysis_type_selector ) == "-tag" :
16 ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}"
17 #else
18 ${analysis_type.analysis_type_selector}
19 #end if
20 -stub split_bam
21 #for $bam_count, $input_bam in enumerate( $input_bams ):
22 -in "localbam_${bam_count}.bam"
23 #end for
24 ]]>
25 </command>
26 <inputs>
27 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
28 <conditional name="analysis_type">
29 <param name="analysis_type_selector" type="select" label="Split BAM dataset(s) by" help="See help below for explanation of each option">
30 <option value="-mapped">Mapping status (-mapped)</option>
31 <option value="-paired">Pairing status (-paired)</option>
32 <option value="-reference">Reference name (-reference)</option>
33 <option value="-tag">Specific tag (-tag)</option>
34 </param>
35 <when value="-mapped" />
36 <when value="-paired" />
37 <when value="-reference" />
38 <when value="-tag">
39 <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter &quot;NM&quot;"/>
40 </when>
41 </conditional>
42 </inputs>
43 <outputs>
44 <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
45 <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
46 </data>
47 </outputs>
48 <tests>
49 <test>
50 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
51 <param name="analysis_type_selector" value="-mapped"/>
52 <output name="report">
53 <assert_contents>
54 <has_line line="BAM" />
55 </assert_contents>
56 <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/>
57 </output>
58 </test>
59 </tests>
60 <help>
61 **What is does**
62
63 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).
64
65 -----
66
67 .. class:: warningmark
68
69 **DANGER: Multiple Outputs**
70
71 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.
72
73 -----
74
75 **How it works**
76
77 The following options can be specified via "**Split BAM dataset(s) by**" dropdown::
78
79 Mapping status (-mapped) split mapped/unmapped and generate two output files
80 named (MAPPED) and (UNMAPPED) containing mapped and unmapped
81 reads, respectively.
82
83 Pairing status (-paired) split single-end/paired-end alignments and generate two output files
84 named (SINGLE_END) and (PAIRED_END) containing paired and unpaired
85 reads, respectively.
86
87 Reference name (-reference) split alignments by reference name. In cases of unfinished genomes with
88 very large number of reference sequences (scaffolds) it can generate
89 thousands (if not millions) of output datasets.
90
91 Specific tag (-tag) split alignments based on all values of TAG encountered. Choosing this
92 option from the menu will allow you to enter the tag name. As was the
93 case with the reference splitting above, this option can produce very
94 large number of outputs if a tag has a large number of unique values.
95
96 -----
97
98 .. class:: infomark
99
100 **More information**
101
102 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
103
104 </help>
105 <citations>
106 <citation type="doi">10.1093/bioinformatics/btr174</citation>
107 </citations>
108 </tool>