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comparison picard_QualityScoreDistribution.xml @ 0:b76a4f17bbbb draft

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author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
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1 <tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="1.122.0">
2 <description>chart quality score distribution</description>
3 <requirements>
4 <requirement type="package" version="1.122.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13 ##set up input files
14
15 #set $reference_fasta_filename = "localref.fa"
16
17 #if str( $reference_source.reference_source_selector ) == "history":
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
19 #else:
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
21 #end if
22
23 java -jar \$JAVA_JAR_PATH/QualityScoreDistribution.jar
24 INPUT="${inputFile}"
25 OUTPUT="${outFile}"
26 CHART_OUTPUT="${pdfFile}"
27 REFERENCE_SEQUENCE="${reference_fasta_filename}"
28 ALIGNED_READS_ONLY="${aligned_reads_only}"
29 PF_READS_ONLY="${pf_reads_only}"
30 INCLUDE_NO_CALLS="${include_no_calls}"
31
32 ASSUME_SORTED="${assume_sorted}"
33
34 VALIDATION_STRINGENCY="${validation_stringency}"
35 QUIET=true
36 VERBOSITY=ERROR
37
38 </command>
39 <inputs>
40 <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"/>
41 <conditional name="reference_source">
42 <param name="reference_source_selector" type="select" label="Load reference genome from">
43 <option value="cached">Local cache</option>
44 <option value="history">History</option>
45 </param>
46 <when value="cached">
47 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
48 <options from_data_table="all_fasta">
49 </options>
50 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
51 </param>
52 </when>
53 <when value="history">
54 <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" />
55 </when>
56 </conditional>
57 <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"/>
58 <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"/>
59 <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"/>
60 <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"/>
61
62 <expand macro="VS" />
63
64 </inputs>
65
66 <outputs>
67 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
68 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
69 </outputs>
70
71 <tests>
72 <test>
73 <param name="assume_sorted" value="true" />
74 <param name="aligned_reads_only" value="false" />
75 <param name="pf_reads_only" value="false" />
76 <param name="include_no_calls" value="false" />
77 <param name="reference_source_selector" value="history" />
78 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
79 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
80 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
81 </test>
82 </tests>
83
84 <stdio>
85 <exit_code range="1:" level="fatal"/>
86 </stdio>
87
88 <help>
89
90 .. class:: infomark
91
92 **Purpose**
93
94 Program to chart quality score distributions in a SAM or BAM dataset.
95
96 @dataset_collections@
97
98 @description@
99
100 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
101 false. Possible values: {true, false}
102
103 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
104 Possible values: {true, false}
105
106 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value:
107 false. Possible values: {true, false}
108
109 ASSUME_SORTED=Boolean
110 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
111
112 @more_info@
113
114 </help>
115 </tool>
116
117