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comparison bamedit.xml @ 1:bbe14234ccdb draft

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author modencode-dcc
date Fri, 18 Jan 2013 10:53:22 -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="package" version="0.1.12">samtools</requirement>
9 </requirements>
10 <description>Merging, splitting, filtering, and QC of BAM files</description>
11 <command interpreter="python">bamedit.py $options_file </command>
12 <inputs>
13 <conditional name="input_type">
14 <param name="input_type_selector" type="select" label="Select your BAM command">
15 <option value="merge">Merge BAM files</option>
16 <option value="split">Split BAM file</option>
17 <option value="filter">Filter BAM file</option>
18 <option value="pileup">Calculate coverage QC</option>
19 </param>
20
21 <when value="merge">
22 <param format="bam" name="input1" type="data" label="Select your first input BAM file"/>
23 <param format="bam" name="input2" type="data" label="Select your second input BAM file"/>
24 <param format="bam" name="input3" type="data" optional="True" label="Select your third input BAM file (optional)" help="Optional third BAM file to be merged."/>
25 </when>
26
27 <when value="split">
28 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
29 </when>
30
31 <when value="filter">
32 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
33 <param name="quality" type="integer" min="1" value="1" label="Minimum Mapping Quality (MMQ)" help="Quality filter should be 1 or higher."/>
34 </when>
35
36 <when value="pileup">
37 <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
38 <param format="fasta" name="input2" type="data" label="Select your fasta reference file"/>
39 <!--<param name="outopt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Alternatative output format" help="format: BAM_FILE, REFERENCE_FILE, GENOME_COVERAGE_PERCENTAGE, AVERAGE_COVERAGE_OF_BASES_COVERED"/>-->
40 </when>
41 </conditional>
42
43 <!--<param name="output_name" type="text" value="output" size="30" label="Output file name"/>-->
44 </inputs>
45
46 <outputs>
47 <data format="bam" name="bamoutm" label="${tool.name}: merge on ${on_string}">
48 <filter>input_type['input_type_selector'] == 'merge'</filter>
49 </data>
50 <data format="bam" name="bamoutf" label="${tool.name}: filter on ${on_string}">
51 <filter> input_type['input_type_selector'] == 'filter'</filter>
52 </data>
53 <data format="bam" name="bamouts1" label="${tool.name}: split on ${on_string} (part 1)">
54 <filter>input_type['input_type_selector'] == 'split'</filter>
55 </data>
56 <data format="bam" name="bamouts2" label="${tool.name}: split on ${on_string} (part2)">
57 <filter>input_type['input_type_selector'] == 'split'</filter>
58 </data>
59 <data format="txt" name="bamoutp" label="${tool.name}: pileup on ${on_string}">
60 <filter>input_type['input_type_selector'] == 'pileup'</filter>
61 </data>
62 </outputs>
63
64 <configfiles>
65 <configfile name="options_file">&lt;%
66 import simplejson
67 %&gt;
68 #if str($input_type.input_type_selector) == 'merge':
69 #if str($input_type.input3) != 'None':
70 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2), 'input3':str($input3) }
71 #else:
72 #set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) }
73 #end if
74 #end if
75 #if str($input_type.input_type_selector) == 'split':
76 #set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
77 #end if
78 #if str($input_type.input_type_selector) == 'filter':
79 #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }
80 #end if
81 #if str($input_type.input_type_selector) == 'pileup':
82 #set $__options = { 'action':str("pileup"), 'bamout':str($bamoutp), 'input1':str($input1), 'input2':str($input2), 'bamname':str($input1.name), 'refname':str($input2.name) }
83 #end if
84 ${ simplejson.dumps( __options )}
85 </configfile>
86 </configfiles>
87 <tests>
88 <test>
89 <!--none -->
90 </test>
91 </tests>
92
93 <help>
94 **What it does**
95
96 Simple interface to manipulate BAM files through the use of SAMtools.
97
98 View the original SAMtools documentation: http://samtools.sourceforge.net/
99
100 ------
101
102 **Usage**
103
104 **Merge BAM files**: Merges 2 or 3 input BAM files into a single BAM file.
105
106 **Split BAM file**: Randomly split input BAM file into 2 BAM files.
107
108 **Filter BAM file**: Removes aligned reads from input BAM files with mapping quality lower than entered Minimum Mapping Quality (MMQ) value.
109
110 **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.
111
112
113 ------
114
115 **Citation**
116
117 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]
118
119 Written by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
120
121 </help>
122 </tool>