annotate picard_CollectWgsMetrics.xml @ 18:7615ac66c6e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 3ce5dea3af8f4816b4a83914b53402aa84e08fca
author iuc
date Sat, 20 Jan 2018 08:28:24 -0500
parents 465cbb0cf2eb
children 5053a18d9bc8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0">
5
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 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
6 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
9 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 ##set up input files
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 #set $reference_fasta_filename = "localref.fa"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
13
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 #if str( $reference_source.reference_source_selector ) == "history":
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 #else:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
19
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
20 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 CollectWgsMetrics
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
22 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 COVERAGE_CAP="${coverage_cap}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
28
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
32
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
33 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 <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
36 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <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
46 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 <when value="history">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 <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
50 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 </conditional>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 <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
53 <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
54 <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
55
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
56
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
58
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 </inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
60
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
64
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <param name="minimum_mapping_quality" value="20" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 <param name="minimum_base_quality" value="20" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <param name="coverage_cap" value="250" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
74 </test>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
76
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
77
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 MINIMUM_MAPPING_QUALITY=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
91 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93 MINIMUM_BASE_QUALITY=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
94 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 COVERAGE_CAP=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
97 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
98 Default value: 250.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105