Mercurial > repos > avowinkel > picard

comparison picard_MeanQualityByCycle.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="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.135">
2 <description>chart distribution of base qualities</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( $reference_source.ref_file.fields.path )
19 #end if
20
21 java -jar \$JAVA_JAR_PATH/picard.jar
22 MeanQualityByCycle
23 INPUT="${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="${pf_reads_only}"
29
30 ASSUME_SORTED="${assume_sorted}"
31
32 VALIDATION_STRINGENCY="${validation_stringency}"
33 QUIET=true
34 VERBOSITY=ERROR
35
36 </command>
37 <inputs>
38 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
39 <conditional name="reference_source">
40 <param name="reference_source_selector" type="select" label="Load reference genome from">
41 <option value="cached">Local cache</option>
42 <option value="history">History</option>
43 </param>
44 <when value="cached">
45 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
46 <options from_data_table="all_fasta">
47 </options>
48 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
49 </param>
50 </when>
51 <when value="history">
52 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
53 </when>
54 </conditional>
55 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
56 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
57 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
58
59 <expand macro="VS" />
60
61 </inputs>
62
63 <outputs>
64 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
65 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
66 </outputs>
67
68 <tests>
69 <test>
70 <param name="assume_sorted" value="true" />
71 <param name="aligned_reads_only" value="false" />
72 <param name="pf_reads_only" value="false" />
73 <param name="reference_source_selector" value="history" />
74 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" />
75 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" />
76 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
77 </test>
78 </tests>
79
80 <stdio>
81 <exit_code range="1:" level="fatal"/>
82 </stdio>
83
84 <help>
85
86 .. class:: infomark
87
88 **Purpose**
89
90 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset.
91
92 @dataset_collections@
93
94 @description@
95
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}
98
99 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
100 This option can be set to 'null' to clear the default value. Possible values: {true,
101 false}
102
103 ASSUME_SORTED=Boolean
104 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
105
106 @more_info@
107
108 </help>
109 </tool>
110
111