|
1
|
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 ${on_string}">
|
|
|
61 <filter>input_type['input_type_selector'] == 'pileup'</filter>
|
|
|
62 </data>
|
|
|
63 </outputs>
|
|
|
64
|
|
|
65 <configfiles>
|
|
|
66 <configfile name="options_file"><%
|
|
|
67 import simplejson
|
|
|
68 %>
|
|
|
69 #if str($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>
|
