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author modencode-dcc
date Fri, 18 Jan 2013 14:48:02 -0500
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1 <!--
2 purpose: xml file for BAMEdit tool
3 author: Ziru Zhou
4 date: October, 2012
5 -->
6 <tool id="BAM_Editor" name="BAMEdit" version="1.1.0">
7 <requirements>
8 <requirement type="set_environment">SCRIPT_PATH</requirement>
9 <requirement type="package" version="0.1.12">samtools</requirement>
10 </requirements>
11 <description>Merging, splitting, filtering, and QC of BAM files</description>
12 <command interpreter="python">bamedit.py $options_file \$SCRIPT_PATH</command>
13 <inputs>
14 <conditional name="input_type">
15 <param name="input_type_selector" type="select" label="Select your BAM command">
16 <option value="merge">Merge BAM files</option>
17 <option value="split">Split BAM file</option>
18 <option value="filter">Filter BAM file</option>
19 <option value="pileup">Calculate coverage QC</option>
20 </param>
21
22 <when value="merge">
23 <param format="bam" name="input1" type="data" label="Select your first input BAM file"/>
24 <param format="bam" name="input2" type="data" label="Select your second input BAM file"/>
25 <param format="bam" name="input3" type="data" optional="True" label="Select your third input BAM file (optional)" help="Optional third BAM file to be merged."/>
26 </when>
27
28 <when value="split">
29 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
30 </when>
31
32 <when value="filter">
33 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
34 <param name="quality" type="integer" min="1" value="1" label="Minimum Mapping Quality (MMQ)" help="Quality filter should be 1 or higher."/>
35 </when>
36
37 <when value="pileup">
38 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
39 <param format="fasta" name="input2" type="data" label="Select your fasta reference file"/>
40 <!--<param name="outopt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Alternatative output format" help="format: BAM_FILE, REFERENCE_FILE, GENOME_COVERAGE_PERCENTAGE, AVERAGE_COVERAGE_OF_BASES_COVERED"/>-->
41 </when>
42 </conditional>
43
44 <!--<param name="output_name" type="text" value="output" size="30" label="Output file name"/>-->
45 </inputs>
46
47 <outputs>
48 <data format="bam" name="bamoutm" label="${tool.name}: merge on ${on_string}">
49 <filter>input_type['input_type_selector'] == 'merge'</filter>
50 </data>
51 <data format="bam" name="bamoutf" label="${tool.name}: filter on ${on_string}">
52 <filter> input_type['input_type_selector'] == 'filter'</filter>
53 </data>
54 <data format="bam" name="bamouts1" label="${tool.name}: split on ${on_string} (part 1)">
55 <filter>input_type['input_type_selector'] == 'split'</filter>
56 </data>
57 <data format="bam" name="bamouts2" label="${tool.name}: split on ${on_string} (part2)">
58 <filter>input_type['input_type_selector'] == 'split'</filter>
59 </data>
60 <data format="txt" name="bamoutp" label="${tool.name}: pileup on ${on_string}">
61 <filter>input_type['input_type_selector'] == 'pileup'</filter>
62 </data>
63 </outputs>
64
65 <configfiles>
66 <configfile name="options_file">&lt;%
67 import simplejson
68 %&gt;
69 #if str($input_type.input_type_selector) == 'merge':
70 #if str($input_type.input3) != 'None':
71 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2), 'input3':str($input3) }
72 #else:
73 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) }
74 #end if
75 #end if
76 #if str($input_type.input_type_selector) == 'split':
77 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
78 #end if
79 #if str($input_type.input_type_selector) == 'filter':
80 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }
81 #end if
82 #if str($input_type.input_type_selector) == 'pileup':
83 #set $__options = { 'action':str("pileup"), 'bamout':str($bamoutp), 'input1':str($input1), 'input2':str($input2), 'bamname':str($input1.name), 'refname':str($input2.name) }
84 #end if
85 ${ simplejson.dumps( __options )}
86 </configfile>
87 </configfiles>
88 <tests>
89 <test>
90 <!--none -->
91 </test>
92 </tests>
93
94 <help>
95 **What it does**
96
97 Simple interface to manipulate BAM files through the use of SAMtools.
98
99 View the original SAMtools documentation: http://samtools.sourceforge.net/
100
101 ------
102
103 **Usage**
104
105 **Merge BAM files**: Merges 2 or 3 input BAM files into a single BAM file.
106
107 **Split BAM file**: Randomly split input BAM file into 2 BAM files.
108
109 **Filter BAM file**: Removes aligned reads from input BAM files with mapping quality lower than entered Minimum Mapping Quality (MMQ) value.
110
111 **Calculate coverage QC**: Calculates QC metrics such as percentage of genome covered and average coverage of bases covered for the input BAM and reference files.
112
113
114 ------
115
116 **Citation**
117
118 Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
119
120 Written by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
121
122 </help>
123 </tool>