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comparison picard_QualityScoreDistribution.xml @ 0:5166ed57b1c4 draft

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Uploaded version 1.135
author avowinkel
date Mon, 06 Jul 2015 14:46:32 -0400
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-1:000000000000 0:5166ed57b1c4
1 <tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="1.135">
2 <description>chart quality score distribution</description>
3 <macros>
4 <import>picard_macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="3.1.2">R</requirement>
8 </expand>
9 <command>
10 @java_options@
11 ##set up input files
12
13 #set $reference_fasta_filename = "localref.fa"
14
15 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
17 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if
20
21 java -jar \$JAVA_JAR_PATH/picard.jar
22 QualityScoreDistribution
23 INPUT="${inputFile}"
24 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}"
26 REFERENCE_SEQUENCE="${reference_fasta_filename}"
27 ALIGNED_READS_ONLY="${aligned_reads_only}"
28 PF_READS_ONLY="${pf_reads_only}"
29 INCLUDE_NO_CALLS="${include_no_calls}"
30
31 ASSUME_SORTED="${assume_sorted}"
32
33 VALIDATION_STRINGENCY="${validation_stringency}"
34 QUIET=true
35 VERBOSITY=ERROR
36
37 </command>
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"/>
40 <conditional name="reference_source">
41 <param name="reference_source_selector" type="select" label="Load reference genome from">
42 <option value="cached">Local cache</option>
43 <option value="history">History</option>
44 </param>
45 <when value="cached">
46 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
47 <options from_data_table="all_fasta">
48 </options>
49 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
50 </param>
51 </when>
52 <when value="history">
53 <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" />
54 </when>
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"/>
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"/>
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
61 <expand macro="VS" />
62
63 </inputs>
64
65 <outputs>
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"/>
68 </outputs>
69
70 <tests>
71 <test>
72 <param name="assume_sorted" value="true" />
73 <param name="aligned_reads_only" value="false" />
74 <param name="pf_reads_only" value="false" />
75 <param name="include_no_calls" value="false" />
76 <param name="reference_source_selector" value="history" />
77 <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" />
78 <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" />
79 <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/>
80 </test>
81 </tests>
82
83 <stdio>
84 <exit_code range="1:" level="fatal"/>
85 </stdio>
86
87 <help>
88
89 .. class:: infomark
90
91 **Purpose**
92
93 Program to chart quality score distributions in a SAM or BAM dataset.
94
95 @dataset_collections@
96
97 @description@
98
99 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
100 false. Possible values: {true, false}
101
102 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
103 Possible values: {true, false}
104
105 INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value:
106 false. Possible values: {true, false}
107
108 ASSUME_SORTED=Boolean
109 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
110
111 @more_info@
112
113 </help>
114 </tool>
115
116