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comparison picard_CollectWgsMetrics.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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32:f9242e01365a 33:3f254c5ced1d
1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>compute metrics for evaluating of whole genome sequencing experiments</description> 2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 @symlink_element_identifier@
11 ##set up input files 11 ##set up input files
12 12
13 #set $reference_fasta_filename = "localref.fa" 13 #set $reference_fasta_filename = "localref.fa"
14 14
15 @handle_reference_source@ 15 @handle_reference_source@
16 16
17 picard 17 picard
18 CollectWgsMetrics 18 CollectWgsMetrics
19 INPUT='$escaped_element_identifier' 19 --INPUT '$escaped_element_identifier'
20 OUTPUT="${outFile}" 20 --OUTPUT '${outFile}'
21 REFERENCE_SEQUENCE="${reference_fasta_filename}" 21 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
22 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" 22 --MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}'
23 MINIMUM_BASE_QUALITY="${minimum_base_quality}" 23 --MINIMUM_BASE_QUALITY '${minimum_base_quality}'
24 COVERAGE_CAP="${coverage_cap}" 24 --COVERAGE_CAP '${coverage_cap}'
25 25
26 VALIDATION_STRINGENCY="${validation_stringency}" 26 --VALIDATION_STRINGENCY '${validation_stringency}'
27 QUIET=true 27 --QUIET true
28 VERBOSITY=ERROR 28 --VERBOSITY ERROR
29 29
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <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"/> 32 <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"/>
33 <conditional name="reference_source"> 33 <conditional name="reference_source">
34 <param name="reference_source_selector" type="select" label="Load reference genome from"> 34 <param name="reference_source_selector" type="select" label="Load reference genome from">
35 <option value="cached">Local cache</option> 35 <option value="cached">Local cache</option>
36 <option value="history">History</option> 36 <option value="history">History</option>
37 </param> 37 </param>
38 <when value="cached"> 38 <when value="cached">
39 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> 39 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
40 <options from_data_table="all_fasta"> 40 <options from_data_table="all_fasta">
41 </options> 41 </options>
42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 42 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
43 </param> 43 </param>
44 </when> 44 </when>
45 <when value="history"> 45 <when value="history">
46 <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" /> 46 <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"/>
47 </when> 47 </when>
48 </conditional> 48 </conditional>
49 <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"/> 49 <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"/>
50 <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"/> 50 <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"/>
51 <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"/> 51 <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"/>
52 52 <expand macro="VS"/>
53 53 </inputs>
54 <expand macro="VS" /> 54 <outputs>
55 55 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
56 </inputs> 56 </outputs>
57 57 <tests>
58 <outputs> 58 <test>
59 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 59 <param name="reference_source_selector" value="history"/>
60 </outputs> 60 <param name="minimum_mapping_quality" value="20"/>
61 61 <param name="minimum_base_quality" value="20"/>
62 <tests> 62 <param name="coverage_cap" value="250"/>
63 <test> 63 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa"/>
64 <param name="reference_source_selector" value="history" /> 64 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam"/>
65 <param name="minimum_mapping_quality" value="20" /> 65 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
66 <param name="minimum_base_quality" value="20" /> 66 </test>
67 <param name="coverage_cap" value="250" /> 67 </tests>
68 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> 68 <help>
69 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
70 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
71 </test>
72 </tests>
73
74
75 <help>
76 69
77 .. class:: infomark 70 .. class:: infomark
78 71
79 **Purpose** 72 **Purpose**
80 73
95 Default value: 250. 88 Default value: 250.
96 89
97 @more_info@ 90 @more_info@
98 91
99 </help> 92 </help>
100 <expand macro="citations" /> 93 <expand macro="citations"/>
101 </tool> 94 </tool>