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comparison picard_CollectAlignmentSummaryMetrics.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
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equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
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 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 @symlink_element_identifier@
9 ##set up input files 10 ##set up input files
10 11
11 #set $reference_fasta_filename = "localref.fa" 12 #set $reference_fasta_filename = "localref.fa"
12 13
13 #if str( $reference_source.reference_source_selector ) == "history": 14 #if str( $reference_source.reference_source_selector ) == "history":
16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
17 #end if 18 #end if
18 19
19 picard 20 picard
20 CollectAlignmentSummaryMetrics 21 CollectAlignmentSummaryMetrics
21 INPUT="${inputFile}" 22 INPUT='$inputFile.element_identifier'
22 OUTPUT="${outFile}" 23 OUTPUT="${outFile}"
23 MAX_INSERT_SIZE=${maxinsert} 24 MAX_INSERT_SIZE=${maxinsert}
24 #for $sequence in $adapters: 25 #for $sequence in $adapters:
25 ADAPTER_SEQUENCE="${sequence.adapter}" 26 ADAPTER_SEQUENCE="${sequence.adapter}"
26 #end for 27 #end for
34 ASSUME_SORTED="${assume_sorted}" 35 ASSUME_SORTED="${assume_sorted}"
35 36
36 VALIDATION_STRINGENCY="${validation_stringency}" 37 VALIDATION_STRINGENCY="${validation_stringency}"
37 QUIET=true 38 QUIET=true
38 VERBOSITY=ERROR 39 VERBOSITY=ERROR
39 40
40 ]]></command> 41 ]]></command>
41 <inputs> 42 <inputs>
42 <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."/> 43 <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."/>
43 <conditional name="reference_source"> 44 <conditional name="reference_source">
44 <param name="reference_source_selector" type="select" label="Load reference genome from"> 45 <param name="reference_source_selector" type="select" label="Load reference genome from">
96 97
97 @dataset_collections@ 98 @dataset_collections@
98 99
99 @description@ 100 @description@
100 101
101 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with 102 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with
102 inter-chromosomal pairs. Default value: 100000. 103 inter-chromosomal pairs. Default value: 100000.
103 104
104 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may 105 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may
105 be specified 0 or more times. 106 be specified 0 or more times.
106 107
107 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel 108 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
108 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, 109 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
109 LIBRARY, READ_GROUP} This option may be specified 0 or more times. 110 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
110 111
111 IS_BISULFITE_SEQUENCED=Boolean 112 IS_BISULFITE_SEQUENCED=Boolean
112 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. 113 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads.
113 114
114 115
115 REFERENCE_SEQUENCE=File 116 REFERENCE_SEQUENCE=File
116 R=File Reference sequence fasta Default value: null. 117 R=File Reference sequence fasta Default value: null.
117 118
118 ASSUME_SORTED=Boolean 119 ASSUME_SORTED=Boolean
119 AS=Boolean If true (default), then the sort order in the header file will be ignored. 120 AS=Boolean If true (default), then the sort order in the header file will be ignored.
120 121
121 @more_info@ 122 @more_info@
122 123
123 </help> 124 </help>
124 </tool> 125 </tool>