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comparison picard_QualityScoreDistribution.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
comparison
equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
7 <requirement type="package" version="3.3.1">r</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @java_options@ 10 @java_options@
11 ##set up input files 11 ##set up input files
12 @symlink_element_identifier@
13 #set $reference_fasta_filename = "localref.fa"
12 14
13 #set $reference_fasta_filename = "localref.fa"
14
15 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
17 #else: 17 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if 19 #end if
20 20
21 picard 21 picard
22 QualityScoreDistribution 22 QualityScoreDistribution
23 INPUT="${inputFile}" 23 INPUT='$inputFile.element_identifier'
24 OUTPUT="${outFile}" 24 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}" 25 CHART_OUTPUT="${pdfFile}"
26 REFERENCE_SEQUENCE="${reference_fasta_filename}" 26 REFERENCE_SEQUENCE="${reference_fasta_filename}"
27 ALIGNED_READS_ONLY="${aligned_reads_only}" 27 ALIGNED_READS_ONLY="${aligned_reads_only}"
28 PF_READS_ONLY="${pf_reads_only}" 28 PF_READS_ONLY="${pf_reads_only}"
29 INCLUDE_NO_CALLS="${include_no_calls}" 29 INCLUDE_NO_CALLS="${include_no_calls}"
30 30
31 ASSUME_SORTED="${assume_sorted}" 31 ASSUME_SORTED="${assume_sorted}"
32 32
33 VALIDATION_STRINGENCY="${validation_stringency}" 33 VALIDATION_STRINGENCY="${validation_stringency}"
34 QUIET=true 34 QUIET=true
35 VERBOSITY=ERROR 35 VERBOSITY=ERROR
36 36
37 ]]></command> 37 ]]></command>
38 <inputs> 38 <inputs>
39 <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"/> 39 <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"/>
40 <conditional name="reference_source"> 40 <conditional name="reference_source">
41 <param name="reference_source_selector" type="select" label="Load reference genome from"> 41 <param name="reference_source_selector" type="select" label="Load reference genome from">
55 </conditional> 55 </conditional>
56 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> 56 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
57 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> 57 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
58 <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/> 58 <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/>
59 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/> 59 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>
60 60
61 <expand macro="VS" /> 61 <expand macro="VS" />
62 62
63 </inputs> 63 </inputs>
64 64
65 <outputs> 65 <outputs>
66 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 66 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
67 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 67 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
68 </outputs> 68 </outputs>
69 69
70 <tests> 70 <tests>
71 <test> 71 <test>
72 <param name="assume_sorted" value="true" /> 72 <param name="assume_sorted" value="true" />
73 <param name="aligned_reads_only" value="false" /> 73 <param name="aligned_reads_only" value="false" />
74 <param name="pf_reads_only" value="false" /> 74 <param name="pf_reads_only" value="false" />
75 <param name="include_no_calls" value="false" /> 75 <param name="include_no_calls" value="false" />
76 <param name="reference_source_selector" value="history" /> 76 <param name="reference_source_selector" value="history" />
77 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" /> 77 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
78 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" /> 78 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
79 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/> 79 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
80 </test> 80 </test>
81 </tests> 81 </tests>
82 82
83 83
84 <help> 84 <help>
85 85
86 .. class:: infomark 86 .. class:: infomark
87 87
88 **Purpose** 88 **Purpose**
91 91
92 @dataset_collections@ 92 @dataset_collections@
93 93
94 @description@ 94 @description@
95 95
96 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: 96 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
97 false. Possible values: {true, false} 97 false. Possible values: {true, false}
98 98
99 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. 99 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
100 Possible values: {true, false} 100 Possible values: {true, false}
101 101
102 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value: 102 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value:
103 false. Possible values: {true, false} 103 false. Possible values: {true, false}
104 104
105 ASSUME_SORTED=Boolean 105 ASSUME_SORTED=Boolean
106 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True 106 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
107 107
108 @more_info@ 108 @more_info@
109 109
110 </help> 110 </help>
111 </tool> 111 </tool>