Mercurial > repos > devteam > picard

comparison picard_CollectWgsMetrics.xml @ 3:52fdfc45590a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
parents
children 08f69add4d06
comparison
equal deleted inserted replaced
2:93ace7e49295 3:52fdfc45590a
1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0">
2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>
8 @java_options@
9 ##set up input files
10
11 #set $reference_fasta_filename = "localref.fa"
12
13 #if str( $reference_source.reference_source_selector ) == "history":
14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
15 #else:
16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
17 #end if
18
19 java -jar \$JAVA_JAR_PATH/picard.jar
20 CollectWgsMetrics
21 INPUT="${inputFile}"
22 OUTPUT="${outFile}"
23 REFERENCE_SEQUENCE="${reference_fasta_filename}"
24 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
25 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
26 COVERAGE_CAP="${coverage_cap}"
27
28 VALIDATION_STRINGENCY="${validation_stringency}"
29 QUIET=true
30 VERBOSITY=ERROR
31
32 </command>
33 <inputs>
34 <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"/>
35 <conditional name="reference_source">
36 <param name="reference_source_selector" type="select" label="Load reference genome from">
37 <option value="cached">Local cache</option>
38 <option value="history">History</option>
39 </param>
40 <when value="cached">
41 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
42 <options from_data_table="all_fasta">
43 </options>
44 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
45 </param>
46 </when>
47 <when value="history">
48 <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" />
49 </when>
50 </conditional>
51 <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"/>
52 <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"/>
53 <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"/>
54
55
56 <expand macro="VS" />
57
58 </inputs>
59
60 <outputs>
61 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
62 </outputs>
63
64 <tests>
65 <test>
66 <param name="reference_source_selector" value="history" />
67 <param name="minimum_mapping_quality" value="20" />
68 <param name="minimum_base_quality" value="20" />
69 <param name="coverage_cap" value="250" />
70 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
71 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
72 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
73 </test>
74 </tests>
75
76 <stdio>
77 <exit_code range="1:" level="fatal"/>
78 </stdio>
79
80 <help>
81
82 .. class:: infomark
83
84 **Purpose**
85
86 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
87
88 @dataset_collections@
89
90 @description@
91
92 MINIMUM_MAPPING_QUALITY=Integer
93 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
94
95 MINIMUM_BASE_QUALITY=Integer
96 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
97
98 COVERAGE_CAP=Integer
99 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
100 Default value: 250.
101
102 @more_info@
103
104 </help>
105 </tool>
106
107