Mercurial > repos > devteam > picard

comparison picard_CollectBaseDistributionByCycle.xml @ 13:7e6fd3d0f16e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
comparison
equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="3.3.1">r</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @java_options@ 10 @java_options@
11 @symlink_element_identifier@
11 ##set up input files 12 ##set up input files
12 13
13 #set $reference_fasta_filename = "localref.fa" 14 #set $reference_fasta_filename = "localref.fa"
14 15
15 #if str( $reference_source.reference_source_selector ) == "history": 16 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
17 #else: 18 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if 20 #end if
20 21
21 picard 22 picard
22 CollectBaseDistributionByCycle 23 CollectBaseDistributionByCycle
23 INPUT="${inputFile}" 24 INPUT='$inputFile.element_identifier'
24 OUTPUT="${outFile}" 25 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}" 26 CHART_OUTPUT="${pdfFile}"
26 ALIGNED_READS_ONLY="${aligned_reads_only}" 27 ALIGNED_READS_ONLY="${aligned_reads_only}"
27 PF_READS_ONLY="${pf_reads_only}" 28 PF_READS_ONLY="${pf_reads_only}"
28 REFERENCE_SEQUENCE="${reference_fasta_filename}" 29 REFERENCE_SEQUENCE="${reference_fasta_filename}"
29 ASSUME_SORTED="${assume_sorted}" 30 ASSUME_SORTED="${assume_sorted}"
30 31
31 VALIDATION_STRINGENCY="${validation_stringency}" 32 VALIDATION_STRINGENCY="${validation_stringency}"
32 QUIET=true 33 QUIET=true
33 VERBOSITY=ERROR 34 VERBOSITY=ERROR
34 35
35 ]]></command> 36 ]]></command>
36 <inputs> 37 <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 <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 <conditional name="reference_source">
39 <param name="reference_source_selector" type="select" label="Load reference genome from"> 40 <param name="reference_source_selector" type="select" label="Load reference genome from">
49 </when> 50 </when>
50 <when value="history"> 51 <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 <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 </when>
53 </conditional> 54 </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="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="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 <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
58 <expand macro="VS" /> 59 <expand macro="VS" />
59 60
60 </inputs> 61 </inputs>
61 62
62 <outputs> 63 <outputs>
63 <data format="tabular" name="outFile"/> 64 <data format="tabular" name="outFile"/>
64 <data format="pdf" name="pdfFile"/> 65 <data format="pdf" name="pdfFile"/>
65 </outputs> 66 </outputs>
66 67
67 <tests> 68 <tests>
68 <test> 69 <test>
69 <param name="aligned_reads_only" value="true" /> 70 <param name="aligned_reads_only" value="true" />
70 <param name="pf_reads_only" value="true" /> 71 <param name="pf_reads_only" value="true" />
71 <param name="assume_sorted" value="true" /> 72 <param name="assume_sorted" value="true" />
73 <param name="ref_file" value="picard_CollectBaseDistributionByCycle_ref.fa" /> 74 <param name="ref_file" value="picard_CollectBaseDistributionByCycle_ref.fa" />
74 <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" /> 75 <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" />
75 <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/> 76 <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
76 </test> 77 </test>
77 </tests> 78 </tests>
78 79
79 80
80 <help> 81 <help>
81 82
82 .. class:: infomark 83 .. class:: infomark
83 84
84 **Purpose** 85 **Purpose**
87 88
88 @dataset_collections@ 89 @dataset_collections@
89 90
90 @description@ 91 @description@
91 92
92 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: 93 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
93 false. This option can be set to 'null' to clear the default value. Possible values: 94 false. This option can be set to 'null' to clear the default value. Possible values:
94 {true, false} 95 {true, false}
95 96
96 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. 97 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
97 This option can be set to 'null' to clear the default value. Possible values: {true, 98 This option can be set to 'null' to clear the default value. Possible values: {true,
98 false} 99 false}
99 100
100 REFERENCE_SEQUENCE=File 101 REFERENCE_SEQUENCE=File
101 R=File Reference sequence fasta Default value: null. 102 R=File Reference sequence fasta Default value: null.
102 103
103 ASSUME_SORTED=Boolean 104 ASSUME_SORTED=Boolean
104 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default 105 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default
105 106
106 @more_info@ 107 @more_info@
107 108
108 </help> 109 </help>
109 </tool> 110 </tool>