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comparison picard_CollectGcBiasMetrics.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 3a3234d7a2e8
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
2 <description>charts the GC bias metrics</description> 2 <description>charts the GC bias metrics</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command> 9 <command detect_errors="exit_code"><![CDATA[
10 @java_options@ 10 @java_options@
11 ##set up input files 11 ##set up input files
12 12
13 #set $reference_fasta_filename = "localref.fa" 13 #set $reference_fasta_filename = "localref.fa"
14 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}" "${reference_fasta_filename}" &amp;&amp; 16 ln -s "${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( $reference_source.ref_file.fields.path )
19 #end if 19 #end if
20 20
21 java -jar \$JAVA_JAR_PATH/picard.jar 21 picard
22 CollectGcBiasMetrics 22 CollectGcBiasMetrics
23 INPUT="${inputFile}" 23 INPUT="${inputFile}"
24 OUTPUT="${outFile}" 24 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}" 25 CHART_OUTPUT="${pdfFile}"
26 SUMMARY_OUTPUT="${summaryFile}" 26 SUMMARY_OUTPUT="${summaryFile}"
27 WINDOW_SIZE="${window_size}" 27 WINDOW_SIZE="${window_size}"
28 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" 28 MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}"
29 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" 29 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
30 REFERENCE_SEQUENCE="${reference_fasta_filename}" 30 REFERENCE_SEQUENCE="${reference_fasta_filename}"
31 ASSUME_SORTED="${assume_sorted}" 31 ASSUME_SORTED="${assume_sorted}"
32 32
33 VALIDATION_STRINGENCY="${validation_stringency}" 33 VALIDATION_STRINGENCY="${validation_stringency}"
34 QUIET=true 34 QUIET=true
35 VERBOSITY=ERROR 35 VERBOSITY=ERROR
36 36
37 </command> 37 ]]></command>
38 <inputs> 38 <inputs>
39 <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."/> 39 <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."/>
40 <conditional name="reference_source"> 40 <conditional name="reference_source">
41 <param name="reference_source_selector" type="select" label="Load reference genome from"> 41 <param name="reference_source_selector" type="select" label="Load reference genome from">
42 <option value="cached">Local cache</option> 42 <option value="cached">Local cache</option>
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" /> 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> 54 </when>
55 </conditional> 55 </conditional>
56 <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/> 56 <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/>
57 <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/> 57 <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/>
58 <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> 58 <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/>
59 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> 59 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
60 60
61 <expand macro="VS" /> 61 <expand macro="VS" />
62 62
63 </inputs> 63 </inputs>
64 64
65 <outputs> 65 <outputs>
66 <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/> 66 <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/>
67 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 67 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
68 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 68 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
69 </outputs> 69 </outputs>
70 70
71 <tests> 71 <tests>
72 <test> 72 <test>
73 <param name="window_size" value="100" /> 73 <param name="window_size" value="100" />
74 <param name="minimum_genome_fraction" value="0.00005" /> 74 <param name="minimum_genome_fraction" value="0.00005" />
75 <param name="assume_sorted" value="true" /> 75 <param name="assume_sorted" value="true" />
76 <param name="is_bisulfite_sequenced" value="true" /> 76 <param name="is_bisulfite_sequenced" value="true" />
77 <param name="reference_source_selector" value="history" /> 77 <param name="reference_source_selector" value="history" />
78 <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" /> 78 <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" />
79 <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" /> 79 <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" />
80 <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 80 <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
81 </test> 81 </test>
82 </tests> 82 </tests>
83 83
84 <stdio> 84
85 <exit_code range="1:" level="fatal"/>
86 </stdio>
87
88 <help> 85 <help>
89 86
90 .. class:: infomark 87 .. class:: infomark
91 88
92 **Purpose** 89 **Purpose**
95 92
96 @dataset_collections@ 93 @dataset_collections@
97 94
98 @description@ 95 @description@
99 96
100 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: 97 ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value:
101 false. Possible values: {true, false} 98 false. Possible values: {true, false}
102 99
103 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. 100 PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false.
104 This option can be set to 'null' to clear the default value. Possible values: {true, 101 This option can be set to 'null' to clear the default value. Possible values: {true,
105 false} 102 false}
106 103
107 ASSUME_SORTED=Boolean 104 ASSUME_SORTED=Boolean
108 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True 105 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
109 106
110 @more_info@ 107 @more_info@
111 108
112 </help> 109 </help>
113 </tool> 110 </tool>