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comparison picard_CollectWgsMetrics.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 @symlink_element_identifier@
9 ##set up input files 10 ##set up input files
10 11
11 #set $reference_fasta_filename = "localref.fa" 12 #set $reference_fasta_filename = "localref.fa"
12 13
13 #if str( $reference_source.reference_source_selector ) == "history": 14 #if str( $reference_source.reference_source_selector ) == "history":
14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
15 #else: 16 #else:
16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
17 #end if 18 #end if
18 19
19 picard 20 picard
20 CollectWgsMetrics 21 CollectWgsMetrics
21 INPUT="${inputFile}" 22 INPUT='$inputFile.element_identifier'
22 OUTPUT="${outFile}" 23 OUTPUT="${outFile}"
23 REFERENCE_SEQUENCE="${reference_fasta_filename}" 24 REFERENCE_SEQUENCE="${reference_fasta_filename}"
24 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" 25 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
25 MINIMUM_BASE_QUALITY="${minimum_base_quality}" 26 MINIMUM_BASE_QUALITY="${minimum_base_quality}"
26 COVERAGE_CAP="${coverage_cap}" 27 COVERAGE_CAP="${coverage_cap}"
27 28
28 VALIDATION_STRINGENCY="${validation_stringency}" 29 VALIDATION_STRINGENCY="${validation_stringency}"
29 QUIET=true 30 QUIET=true
30 VERBOSITY=ERROR 31 VERBOSITY=ERROR
31 32
32 ]]></command> 33 ]]></command>
33 <inputs> 34 <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 <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 <conditional name="reference_source">
36 <param name="reference_source_selector" type="select" label="Load reference genome from"> 37 <param name="reference_source_selector" type="select" label="Load reference genome from">
50 </conditional> 51 </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_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="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 <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
55 56
56 <expand macro="VS" /> 57 <expand macro="VS" />
57 58
58 </inputs> 59 </inputs>
59 60
60 <outputs> 61 <outputs>
61 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 62 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
62 </outputs> 63 </outputs>
63 64
64 <tests> 65 <tests>
65 <test> 66 <test>
66 <param name="reference_source_selector" value="history" /> 67 <param name="reference_source_selector" value="history" />
67 <param name="minimum_mapping_quality" value="20" /> 68 <param name="minimum_mapping_quality" value="20" />
68 <param name="minimum_base_quality" value="20" /> 69 <param name="minimum_base_quality" value="20" />
69 <param name="coverage_cap" value="250" /> 70 <param name="coverage_cap" value="250" />
70 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> 71 <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
71 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> 72 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
72 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 73 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
73 </test> 74 </test>
74 </tests> 75 </tests>
75 76
76 77
77 <help> 78 <help>
78 79
79 .. class:: infomark 80 .. class:: infomark
80 81
81 **Purpose** 82 **Purpose**
85 @dataset_collections@ 86 @dataset_collections@
86 87
87 @description@ 88 @description@
88 89
89 MINIMUM_MAPPING_QUALITY=Integer 90 MINIMUM_MAPPING_QUALITY=Integer
90 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. 91 MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20.
91 92
92 MINIMUM_BASE_QUALITY=Integer 93 MINIMUM_BASE_QUALITY=Integer
93 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. 94 Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20.
94 95
95 COVERAGE_CAP=Integer 96 COVERAGE_CAP=Integer
96 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. 97 CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value.
97 Default value: 250. 98 Default value: 250.
98 99
99 @more_info@ 100 @more_info@
100 101
101 </help> 102 </help>
102 </tool> 103 </tool>