|
5
|
1 <tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="1.126.0">
|
|
|
2 <description>chart quality score distribution</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.126.0">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}" &&
|
|
|
19 #else:
|
|
|
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
|
|
|
21 #end if
|
|
|
22
|
|
|
23 java -jar \$JAVA_JAR_PATH/picard.jar
|
|
|
24 QualityScoreDistribution
|
|
|
25 INPUT="${inputFile}"
|
|
|
26 OUTPUT="${outFile}"
|
|
|
27 CHART_OUTPUT="${pdfFile}"
|
|
|
28 REFERENCE_SEQUENCE="${reference_fasta_filename}"
|
|
|
29 ALIGNED_READS_ONLY="${aligned_reads_only}"
|
|
|
30 PF_READS_ONLY="${pf_reads_only}"
|
|
|
31 INCLUDE_NO_CALLS="${include_no_calls}"
|
|
|
32
|
|
|
33 ASSUME_SORTED="${assume_sorted}"
|
|
|
34
|
|
|
35 VALIDATION_STRINGENCY="${validation_stringency}"
|
|
|
36 QUIET=true
|
|
|
37 VERBOSITY=ERROR
|
|
|
38
|
|
|
39 </command>
|
|
|
40 <inputs>
|
|
|
41 <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"/>
|
|
|
42 <conditional name="reference_source">
|
|
|
43 <param name="reference_source_selector" type="select" label="Load reference genome from">
|
|
|
44 <option value="cached">Local cache</option>
|
|
|
45 <option value="history">History</option>
|
|
|
46 </param>
|
|
|
47 <when value="cached">
|
|
|
48 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
|
|
|
49 <options from_data_table="all_fasta">
|
|
|
50 </options>
|
|
|
51 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
|
|
|
52 </param>
|
|
|
53 </when>
|
|
|
54 <when value="history">
|
|
|
55 <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" />
|
|
|
56 </when>
|
|
|
57 </conditional>
|
|
|
58 <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"/>
|
|
|
59 <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"/>
|
|
|
60 <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"/>
|
|
|
61 <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"/>
|
|
|
62
|
|
|
63 <expand macro="VS" />
|
|
|
64
|
|
|
65 </inputs>
|
|
|
66
|
|
|
67 <outputs>
|
|
|
68 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
|
|
|
69 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
|
|
|
70 </outputs>
|
|
|
71
|
|
|
72 <tests>
|
|
|
73 <test>
|
|
|
74 <param name="assume_sorted" value="true" />
|
|
|
75 <param name="aligned_reads_only" value="false" />
|
|
|
76 <param name="pf_reads_only" value="false" />
|
|
|
77 <param name="include_no_calls" value="false" />
|
|
|
78 <param name="reference_source_selector" value="history" />
|
|
|
79 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
|
|
|
80 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
|
|
|
81 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
|
|
|
82 </test>
|
|
|
83 </tests>
|
|
|
84
|
|
|
85 <stdio>
|
|
|
86 <exit_code range="1:" level="fatal"/>
|
|
|
87 </stdio>
|
|
|
88
|
|
|
89 <help>
|
|
|
90
|
|
|
91 .. class:: infomark
|
|
|
92
|
|
|
93 **Purpose**
|
|
|
94
|
|
|
95 Program to chart quality score distributions in a SAM or BAM dataset.
|
|
|
96
|
|
|
97 @dataset_collections@
|
|
|
98
|
|
|
99 @description@
|
|
|
100
|
|
|
101 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
|
|
|
102 false. Possible values: {true, false}
|
|
|
103
|
|
|
104 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
|
|
|
105 Possible values: {true, false}
|
|
|
106
|
|
|
107 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value:
|
|
|
108 false. Possible values: {true, false}
|
|
|
109
|
|
|
110 ASSUME_SORTED=Boolean
|
|
|
111 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
|
|
|
112
|
|
|
113 @more_info@
|
|
|
114
|
|
|
115 </help>
|
|
|
116 </tool>
|
|
|
117
|
|
|
118
|
