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comparison picard_MeanQualityByCycle.xml @ 13:7e6fd3d0f16e draft

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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
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 ##set up input files 11 ##set up input files
12 @symlink_element_identifier@
13 #set $reference_fasta_filename = "localref.fa"
12 14
13 #set $reference_fasta_filename = "localref.fa"
14
15 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
17 #else: 17 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if 19 #end if
20 20
21 picard 21 picard
22 MeanQualityByCycle 22 MeanQualityByCycle
23 INPUT="${inputFile}" 23 INPUT='$inputFile.element_identifier'
24 OUTPUT="${outFile}" 24 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}" 25 CHART_OUTPUT="${pdfFile}"
26 REFERENCE_SEQUENCE="${reference_fasta_filename}" 26 REFERENCE_SEQUENCE="${reference_fasta_filename}"
27 ALIGNED_READS_ONLY="${aligned_reads_only}" 27 ALIGNED_READS_ONLY="${aligned_reads_only}"
28 PF_READS_ONLY="${pf_reads_only}" 28 PF_READS_ONLY="${pf_reads_only}"
29 29
30 ASSUME_SORTED="${assume_sorted}" 30 ASSUME_SORTED="${assume_sorted}"
31 31
32 VALIDATION_STRINGENCY="${validation_stringency}" 32 VALIDATION_STRINGENCY="${validation_stringency}"
33 QUIET=true 33 QUIET=true
34 VERBOSITY=ERROR 34 VERBOSITY=ERROR
35 35
36 ]]></command> 36 ]]></command>
37 <inputs> 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."/> 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"> 39 <conditional name="reference_source">
40 <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">
53 </when> 53 </when>
54 </conditional> 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"/> 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"/> 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"/> 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 58
59 <expand macro="VS" /> 59 <expand macro="VS" />
60 60
61 </inputs> 61 </inputs>
62 62
63 <outputs> 63 <outputs>
64 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 64 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
65 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 65 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
66 </outputs> 66 </outputs>
67 67
68 <tests> 68 <tests>
69 <test> 69 <test>
70 <param name="assume_sorted" value="true" /> 70 <param name="assume_sorted" value="true" />
71 <param name="aligned_reads_only" value="false" /> 71 <param name="aligned_reads_only" value="false" />
72 <param name="pf_reads_only" value="false" /> 72 <param name="pf_reads_only" value="false" />
73 <param name="reference_source_selector" value="history" /> 73 <param name="reference_source_selector" value="history" />
74 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> 74 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" />
75 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> 75 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" />
76 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/> 76 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
77 </test> 77 </test>
78 </tests> 78 </tests>
79 79
80 80
81 <help> 81 <help>
82 82
83 .. class:: infomark 83 .. class:: infomark
84 84
85 **Purpose** 85 **Purpose**
86 86
87 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. 87 Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset.
88 88
89 @dataset_collections@ 89 @dataset_collections@
90 90
91 @description@ 91 @description@
92 92
93 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:
94 false. Possible values: {true, false} 94 false. Possible values: {true, false}
95 95
96 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. 96 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, 97 This option can be set to 'null' to clear the default value. Possible values: {true,
98 false} 98 false}
99 99
100 ASSUME_SORTED=Boolean 100 ASSUME_SORTED=Boolean
101 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True 101 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
102 102
103 @more_info@ 103 @more_info@
104 104
105 </help> 105 </help>
106 </tool> 106 </tool>