annotate picard_CollectAlignmentSummaryMetrics.xml @ 6:4ff1e04010e6 draft

Uploaded
author devteam
date Thu, 15 Jan 2015 15:37:04 -0500
parents 3d4f1fa26f0e
children 3a3234d7a2e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
1 <tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>writes a file containing summary alignment metrics</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <requirements>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <requirement type="package" version="1.126.0">picard</requirement>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </requirements>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
7 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 </macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 <command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 ##set up input files
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 #set $reference_fasta_filename = "localref.fa"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 #if str( $reference_source.reference_source_selector ) == "history":
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 #else:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 #end if
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 CollectAlignmentSummaryMetrics
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 INPUT="${inputFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 MAX_INSERT_SIZE=${maxinsert}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 #for $sequence in $adapters:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 ADAPTER_SEQUENCE="${sequence.adapter}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 IS_BISULFITE_SEQUENCED="${bisulphite}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 REFERENCE_SEQUENCE="${reference_fasta_filename}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 ASSUME_SORTED="${assume_sorted}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <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."/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <conditional name="reference_source">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <param name="reference_source_selector" type="select" label="Load reference genome from">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <option value="cached">Local cache</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 <option value="history">History</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <when value="cached">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 <options from_data_table="all_fasta">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 </options>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 <when value="history">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 <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" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 </conditional>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 <option value="ALL_READS" selected="True">All reads</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 <option value="SAMPLE">Sample</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 <option value="LIBRARY">Library</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 <option value="READ_GROUP">Read group</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72 <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89 <param name="bisulphite" value="false" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 <param name="sorted" value="true" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91 <param name="adaptors" value="" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 <param name="maxinsert" value="100000" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93 <param name="reference_source_selector" value="history" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 <param name="ref_file" value="picard_CASM_ref.fa" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95 <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
96 <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
103
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
104 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
106 Reads a SAM or BAM file and writes a file containing summary alignment metrics.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
107
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
109
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
111
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
112 MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
113 inter-chromosomal pairs. Default value: 100000.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
114
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
115 ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
116 be specified 0 or more times.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
117
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
118 METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
119 LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE,
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
120 LIBRARY, READ_GROUP} This option may be specified 0 or more times.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
121
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
122 IS_BISULFITE_SEQUENCED=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
123 BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
124
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
125
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
126 REFERENCE_SEQUENCE=File
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
127 R=File Reference sequence fasta Default value: null.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
128
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
129 ASSUME_SORTED=Boolean
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
130 AS=Boolean If true (default), then the sort order in the header file will be ignored.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
131
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
132 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
133
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
134 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
135 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
136
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
137