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comparison picard_AddOrReplaceReadGroups.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="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.122.0">
2 <description>add or replaces read group information</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 java -jar \$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar
14 INPUT="${inputFile}"
15 RGLB="${rglb}"
16 RGPL="${rgpl}"
17 RGPU="${rgpu}"
18 RGSM="${rgsm}"
19 RGID="${rgid}"
20
21 #if str( $rgcn):
22 RGCN="${rgcn}"
23 #end if
24
25 #if str( $rgds):
26 RGDS="${rgds}"
27 #end if
28
29 #if str( $rgpi):
30 RGPI="${rgpi}"
31 #end if
32
33 #if str( $rgdt):
34 RGDT="${rgdt}"
35 #end if
36
37 VALIDATION_STRINGENCY="${validation_stringency}"
38 QUIET=true
39 VERBOSITY=ERROR
40 OUTPUT="${outFile}"
41
42 </command>
43
44 <inputs>
45 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
46 <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" />
47 <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" />
48 <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" />
49 <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" />
50 <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" />
51 <!-- optional params -->
52 <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" />
53 <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" />
54 <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" />
55 <param name="rgdt" value="" optional="True" type="text" label="Read Group run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
56
57 <expand macro="VS" />
58
59 </inputs>
60
61 <outputs>
62 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
63 </outputs>
64
65 <stdio>
66 <exit_code range="1:" level="fatal"/>
67 </stdio>
68
69 <tests>
70 <test>
71 <param name="inputFile" value="picard_ARRG.bam" />
72 <param name="rglb" value="tumor-a" />
73 <param name="rgpl" value="Illumina" />
74 <param name="rgpu" value="run-1" />
75 <param name="rgsm" value="sample-a" />
76 <param name="rgid" value="id-1" />
77 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
78 </test>
79 </tests>
80 <help>
81
82 .. class:: infomark
83
84 **Purpose**
85
86 Add or Replace Read Groups in an input BAM or SAM file.
87
88 @dataset_collections@
89
90 @RG@
91
92 @description@
93
94 INPUT=File
95 I=File Input file (bam or sam). Required.
96
97 OUTPUT=File
98 O=File Output file (bam or sam). Required.
99
100 SORT_ORDER=SortOrder
101 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
102 Default value: null. Possible values: {unsorted, queryname, coordinate}
103
104 RGID=String
105 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
106 value.
107
108 RGLB=String
109 LB=String Read Group Library Required.
110
111 RGPL=String
112 PL=String Read Group platform (e.g. illumina, solid) Required.
113
114 RGPU=String
115 PU=String Read Group platform unit (eg. run barcode) Required.
116
117 RGSM=String
118 SM=String Read Group sample name Required.
119
120 RGCN=String
121 CN=String Read Group sequencing center name Default value: null.
122
123 RGDS=String
124 DS=String Read Group description Default value: null.
125
126 RGDT=Iso8601Date
127 DT=Iso8601Date Read Group run date Default value: null.
128
129 RGPI=Integer
130 PI=Integer Read Group predicted insert size Default value: null.
131
132 @more_info@
133 </help>
134 </tool>
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