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comparison picard_CollectWgsMetrics.xml @ 5:3d4f1fa26f0e draft

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author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
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4:ab1f60c26526 5:3d4f1fa26f0e
1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="1.126.0">
2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13 ##set up input files
14
15 #set $reference_fasta_filename = "localref.fa"
16
17 #if str( $reference_source.reference_source_selector ) == "history":
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
19 #else:
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
21 #end if
22
23 java -jar \$JAVA_JAR_PATH/picard.jar
24 CollectWgsMetrics
25 INPUT="${inputFile}"
26 OUTPUT="${outFile}"
27 REFERENCE_SEQUENCE="${reference_fasta_filename}"
28 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
29 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
30 COVERAGE_CAP="${coverage_cap}"
31
32 VALIDATION_STRINGENCY="${validation_stringency}"
33 QUIET=true
34 VERBOSITY=ERROR
35
36 </command>
37 <inputs>
38 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
39 <conditional name="reference_source">
40 <param name="reference_source_selector" type="select" label="Load reference genome from">
41 <option value="cached">Local cache</option>
42 <option value="history">History</option>
43 </param>
44 <when value="cached">
45 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
46 <options from_data_table="all_fasta">
47 </options>
48 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
49 </param>
50 </when>
51 <when value="history">
52 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
53 </when>
54 </conditional>
55 <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/>
56 <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
57 <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
58
59
60 <expand macro="VS" />
61
62 </inputs>
63
64 <outputs>
65 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
66 </outputs>
67
68 <tests>
69 <test>
70 <param name="reference_source_selector" value="history" />
71 <param name="minimum_mapping_quality" value="20" />
72 <param name="minimum_base_quality" value="20" />
73 <param name="coverage_cap" value="250" />
74 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
75 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
76 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
77 </test>
78 </tests>
79
80 <stdio>
81 <exit_code range="1:" level="fatal"/>
82 </stdio>
83
84 <help>
85
86 .. class:: infomark
87
88 **Purpose**
89
90 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
91
92 @dataset_collections@
93
94 @description@
95
96 MINIMUM_MAPPING_QUALITY=Integer
97 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
98
99 MINIMUM_BASE_QUALITY=Integer
100 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
101
102 COVERAGE_CAP=Integer
103 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
104 Default value: 250.
105
106 @more_info@
107
108 </help>
109 </tool>
110
111