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comparison picard_CollectBaseDistributionByCycle.xml @ 3:52fdfc45590a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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2:93ace7e49295 3:52fdfc45590a
1 <tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="@TOOL_VERSION@.0">
2 <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</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( $reference_source.ref_file.fields.path )
19 #end if
20
21 java -jar \$JAVA_JAR_PATH/picard.jar
22 CollectBaseDistributionByCycle
23 INPUT="${inputFile}"
24 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}"
26 ALIGNED_READS_ONLY="${aligned_reads_only}"
27 PF_READS_ONLY="${pf_reads_only}"
28 REFERENCE_SEQUENCE="${reference_fasta_filename}"
29 ASSUME_SORTED="${assume_sorted}"
30
31 VALIDATION_STRINGENCY="${validation_stringency}"
32 QUIET=true
33 VERBOSITY=ERROR
34
35 </command>
36 <inputs>
37 <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."/>
38 <conditional name="reference_source">
39 <param name="reference_source_selector" type="select" label="Load reference genome from">
40 <option value="cached">Local cache</option>
41 <option value="history">History</option>
42 </param>
43 <when value="cached">
44 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
45 <options from_data_table="all_fasta">
46 </options>
47 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
48 </param>
49 </when>
50 <when value="history">
51 <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" />
52 </when>
53 </conditional>
54 <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/>
55 <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/>
56 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
57
58 <expand macro="VS" />
59
60 </inputs>
61
62 <outputs>
63 <data format="tabular" name="outFile"/>
64 <data format="pdf" name="pdfFile"/>
65 </outputs>
66
67 <tests>
68 <test>
69 <param name="aligned_reads_only" value="true" />
70 <param name="pf_reads_only" value="true" />
71 <param name="assume_sorted" value="true" />
72 <param name="reference_source_selector" value="history" />
73 <param name="ref_file" value="picard_CollectBaseDistributionByCycle_ref.fa" />
74 <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" />
75 <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
76 </test>
77 </tests>
78
79 <stdio>
80 <exit_code range="1:" level="fatal"/>
81 </stdio>
82
83 <help>
84
85 .. class:: infomark
86
87 **Purpose**
88
89 Program to chart the nucleotide distribution per cycle in a SAM or BAM file.
90
91 @dataset_collections@
92
93 @description@
94
95 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
96 false. This option can be set to 'null' to clear the default value. Possible values:
97 {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 REFERENCE_SEQUENCE=File
104 R=File Reference sequence fasta Default value: null.
105
106 ASSUME_SORTED=Boolean
107 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
108
109 @more_info@
110
111 </help>
112 </tool>
113
114