annotate picard_CollectWgsMetrics.xml @ 5:3d4f1fa26f0e draft

Uploaded
author devteam
date Tue, 16 Dec 2014 19:03:21 -0500
parents
children 3a3234d7a2e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="1.126.0">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <requirements>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <requirement type="package" version="1.126.0">picard</requirement>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </requirements>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
7 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 </macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 <command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 ##set up input files
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 #set $reference_fasta_filename = "localref.fa"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 #if str( $reference_source.reference_source_selector ) == "history":
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 #else:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 #end if
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 CollectWgsMetrics
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 INPUT="${inputFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 COVERAGE_CAP="${coverage_cap}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <when value="history">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 </conditional>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
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"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <param name="minimum_mapping_quality" value="20" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="minimum_base_quality" value="20" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <param name="coverage_cap" value="250" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 MINIMUM_MAPPING_QUALITY=Integer
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99 MINIMUM_BASE_QUALITY=Integer
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 COVERAGE_CAP=Integer
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104 Default value: 250.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
107
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
109 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
111