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comparison picard_MeanQualityByCycle.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="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.122.0">
2 <description>chart distribution of base qualities</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( $reference_source.ref_file.fields.path )
21 #end if
22
23 java -jar \$JAVA_JAR_PATH/MeanQualityByCycle.jar
24 INPUT="${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="${pf_reads_only}"
30
31 ASSUME_SORTED="${assume_sorted}"
32
33 VALIDATION_STRINGENCY="${validation_stringency}"
34 QUIET=true
35 VERBOSITY=ERROR
36
37 </command>
38 <inputs>
39 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
40 <conditional name="reference_source">
41 <param name="reference_source_selector" type="select" label="Load reference genome from">
42 <option value="cached">Local cache</option>
43 <option value="history">History</option>
44 </param>
45 <when value="cached">
46 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
47 <options from_data_table="all_fasta">
48 </options>
49 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
50 </param>
51 </when>
52 <when value="history">
53 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
54 </when>
55 </conditional>
56 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
57 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
58 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
59
60 <expand macro="VS" />
61
62 </inputs>
63
64 <outputs>
65 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
66 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
67 </outputs>
68
69 <tests>
70 <test>
71 <param name="assume_sorted" value="true" />
72 <param name="aligned_reads_only" value="false" />
73 <param name="pf_reads_only" value="false" />
74 <param name="reference_source_selector" value="history" />
75 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" />
76 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" />
77 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
78 </test>
79 </tests>
80
81 <stdio>
82 <exit_code range="1:" level="fatal"/>
83 </stdio>
84
85 <help>
86
87 .. class:: infomark
88
89 **Purpose**
90
91 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset.
92
93 @dataset_collections@
94
95 @description@
96
97 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
98 false. Possible values: {true, false}
99
100 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
101 This option can be set to 'null' to clear the default value. Possible values: {true,
102 false}
103
104 ASSUME_SORTED=Boolean
105 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
106
107 @more_info@
108
109 </help>
110 </tool>
111
112