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comparison picard_CollectAlignmentSummaryMetrics.xml @ 0:b76a4f17bbbb draft

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author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
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1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.122.0">
2 <description>writes a file containing summary alignment metrics</description>
3 <requirements>
4 <requirement type="package" version="1.122.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13 ##set up input files
14
15 #set $reference_fasta_filename = "localref.fa"
16
17 #if str( $reference_source.reference_source_selector ) == "history":
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
19 #else:
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
21 #end if
22
23 java -jar \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar
24 INPUT="${inputFile}"
25 OUTPUT="${outFile}"
26 MAX_INSERT_SIZE=${maxinsert}
27 #for $sequence in $adapters:
28 ADAPTER_SEQUENCE="${sequence.adapter}"
29 #end for
30 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
31 IS_BISULFITE_SEQUENCED="${bisulphite}"
32
33 REFERENCE_SEQUENCE="${reference_fasta_filename}"
34
35 ASSUME_SORTED="${assume_sorted}"
36
37 VALIDATION_STRINGENCY="${validation_stringency}"
38 QUIET=true
39 VERBOSITY=ERROR
40
41 </command>
42 <inputs>
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."/>
44 <conditional name="reference_source">
45 <param name="reference_source_selector" type="select" label="Load reference genome from">
46 <option value="cached">Local cache</option>
47 <option value="history">History</option>
48 </param>
49 <when value="cached">
50 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
51 <options from_data_table="all_fasta">
52 </options>
53 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
54 </param>
55 </when>
56 <when value="history">
57 <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" />
58 </when>
59 </conditional>
60 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
61 <option value="ALL_READS" selected="True">All reads</option>
62 <option value="SAMPLE">Sample</option>
63 <option value="LIBRARY">Library</option>
64 <option value="READ_GROUP">Read group</option>
65 </param>
66 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
67 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
68 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
69 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
70 </repeat>
71 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/>
72
73 <expand macro="VS" />
74
75 </inputs>
76
77 <outputs>
78 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
79 </outputs>
80
81 <stdio>
82 <exit_code range="1:" level="fatal"/>
83 </stdio>
84
85
86 <tests>
87 <test>
88 <param name="bisulphite" value="false" />
89 <param name="sorted" value="true" />
90 <param name="adaptors" value="" />
91 <param name="maxinsert" value="100000" />
92 <param name="reference_source_selector" value="history" />
93 <param name="ref_file" value="picard_CASM_ref.fa" />
94 <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
95 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
96 </test>
97 </tests>
98
99 <help>
100
101 .. class:: infomark
102
103 **Purpose**
104
105 Reads a SAM or BAM file and writes a file containing summary alignment metrics.
106
107 @dataset_collections@
108
109 @description@
110
111 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with
112 inter-chromosomal pairs. Default value: 100000.
113
114 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may
115 be specified 0 or more times.
116
117 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
118 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
119 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
120
121 IS_BISULFITE_SEQUENCED=Boolean
122 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads.
123
124
125 REFERENCE_SEQUENCE=File
126 R=File Reference sequence fasta Default value: null.
127
128 ASSUME_SORTED=Boolean
129 AS=Boolean If true (default), then the sort order in the header file will be ignored.
130
131 @more_info@
132
133 </help>
134 </tool>
135
136