Mercurial > repos > modencode-dcc > bamedit
comparison bamedit.xml @ 12:7a51d316635a draft
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author | modencode-dcc |
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date | Fri, 18 Jan 2013 15:55:46 -0500 |
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11:f5e6e4a22981 | 12:7a51d316635a |
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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 <requirement type="package" version="0.1.12">maq2sam-long</requirement> | |
11 </requirements> | |
12 <description>Merging, splitting, filtering, and QC of BAM files</description> | |
13 <command interpreter="python">bamedit.py $options_file \$SCRIPT_PATH</command> | |
14 <inputs> | |
15 <conditional name="input_type"> | |
16 <param name="input_type_selector" type="select" label="Select your BAM command"> | |
17 <option value="merge">Merge BAM files</option> | |
18 <option value="split">Split BAM file</option> | |
19 <option value="filter">Filter BAM file</option> | |
20 <option value="pileup">Calculate coverage QC</option> | |
21 </param> | |
22 | |
23 <when value="merge"> | |
24 <param format="bam" name="input1" type="data" label="Select your first input BAM file"/> | |
25 <param format="bam" name="input2" type="data" label="Select your second input BAM file"/> | |
26 <param format="bam" name="input3" type="data" optional="True" label="Select your third input BAM file (optional)" help="Optional third BAM file to be merged."/> | |
27 </when> | |
28 | |
29 <when value="split"> | |
30 <param format="bam" name="input1" type="data" label="Select your input BAM file"/> | |
31 </when> | |
32 | |
33 <when value="filter"> | |
34 <param format="bam" name="input1" type="data" label="Select your input BAM file"/> | |
35 <param name="quality" type="integer" min="1" value="1" label="Minimum Mapping Quality (MMQ)" help="Quality filter should be 1 or higher."/> | |
36 </when> | |
37 | |
38 <when value="pileup"> | |
39 <param format="bam" name="input1" type="data" label="Select your input BAM file"/> | |
40 <param format="fasta" name="input2" type="data" label="Select your fasta reference file"/> | |
41 <!--<param name="outopt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Alternatative output format" help="format: BAM_FILE, REFERENCE_FILE, GENOME_COVERAGE_PERCENTAGE, AVERAGE_COVERAGE_OF_BASES_COVERED"/>--> | |
42 </when> | |
43 </conditional> | |
44 | |
45 <!--<param name="output_name" type="text" value="output" size="30" label="Output file name"/>--> | |
46 </inputs> | |
47 | |
48 <outputs> | |
49 <data format="bam" name="bamoutm" label="${tool.name}: merge on ${on_string}"> | |
50 <filter>input_type['input_type_selector'] == 'merge'</filter> | |
51 </data> | |
52 <data format="bam" name="bamoutf" label="${tool.name}: filter on ${on_string}"> | |
53 <filter> input_type['input_type_selector'] == 'filter'</filter> | |
54 </data> | |
55 <data format="bam" name="bamouts1" label="${tool.name}: split on ${on_string} (part 1)"> | |
56 <filter>input_type['input_type_selector'] == 'split'</filter> | |
57 </data> | |
58 <data format="bam" name="bamouts2" label="${tool.name}: split on ${on_string} (part2)"> | |
59 <filter>input_type['input_type_selector'] == 'split'</filter> | |
60 </data> | |
61 <data format="txt" name="bamoutp" label="${tool.name}: pileup on ${on_string}"> | |
62 <filter>input_type['input_type_selector'] == 'pileup'</filter> | |
63 </data> | |
64 </outputs> | |
65 | |
66 <configfiles> | |
67 <configfile name="options_file"><% | |
68 import simplejson | |
69 %> | |
70 #if str($input_type.input_type_selector) == 'merge': | |
71 #if str($input_type.input3) != 'None': | |
72 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2), 'input3':str($input3) } | |
73 #else: | |
74 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) } | |
75 #end if | |
76 #end if | |
77 #if str($input_type.input_type_selector) == 'split': | |
78 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) } | |
79 #end if | |
80 #if str($input_type.input_type_selector) == 'filter': | |
81 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) } | |
82 #end if | |
83 #if str($input_type.input_type_selector) == 'pileup': | |
84 #set $__options = { 'action':str("pileup"), 'bamout':str($bamoutp), 'input1':str($input1), 'input2':str($input2), 'bamname':str($input1.name), 'refname':str($input2.name) } | |
85 #end if | |
86 ${ simplejson.dumps( __options )} | |
87 </configfile> | |
88 </configfiles> | |
89 <tests> | |
90 <test> | |
91 <!--none --> | |
92 </test> | |
93 </tests> | |
94 | |
95 <help> | |
96 **What it does** | |
97 | |
98 Simple interface to manipulate BAM files through the use of SAMtools. | |
99 | |
100 View the original SAMtools documentation: http://samtools.sourceforge.net/ | |
101 | |
102 ------ | |
103 | |
104 **Usage** | |
105 | |
106 **Merge BAM files**: Merges 2 or 3 input BAM files into a single BAM file. | |
107 | |
108 **Split BAM file**: Randomly split input BAM file into 2 BAM files. | |
109 | |
110 **Filter BAM file**: Removes aligned reads from input BAM files with mapping quality lower than entered Minimum Mapping Quality (MMQ) value. | |
111 | |
112 **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. | |
113 | |
114 | |
115 ------ | |
116 | |
117 **Citation** | |
118 | |
119 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] | |
120 | |
121 Written by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org. | |
122 | |
123 </help> | |
124 </tool> |