|
5
|
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}" &&
|
|
|
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
|
