annotate picard_AddOrReplaceReadGroups.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: 2
diff changeset
1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.126.0">
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
2 <description>add or replaces read group information</description>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
3 <requirements>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
4 <requirement type="package" version="1.126.0">picard</requirement>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
5 </requirements>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
6
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
7 <macros>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
8 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
9 </macros>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
10
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
11 <command>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
12 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
13 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
14 AddOrReplaceReadGroups
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
15 INPUT="${inputFile}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
16 RGLB="${rglb}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
17 RGPL="${rgpl}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
18 RGPU="${rgpu}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
19 RGSM="${rgsm}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
20 RGID="${rgid}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
21
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
22 #if str( $rgcn):
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
23 RGCN="${rgcn}"
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
24 #end if
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
25
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
26 #if str( $rgds):
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
27 RGDS="${rgds}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
28 #end if
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
29
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
30 #if str( $rgpi):
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
31 RGPI="${rgpi}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
32 #end if
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
33
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
34 #if str( $rgdt):
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
35 RGDT="${rgdt}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
36 #end if
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
37
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
38 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
39 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
40 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
41 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
42
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
43 </command>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
44
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
45 <inputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
46 <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" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
47 <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
48 <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
49 <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
50 <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
51 <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
52 <!-- optional params -->
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
53 <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
54 <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
55 <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
56 <param name="rgdt" value="" optional="True" type="text" label="Read Group run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
57
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
58 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
59
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
60 </inputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
61
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
62 <outputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
63 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
64 </outputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
65
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
66 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
67 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
68 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
69
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
70 <tests>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
71 <test>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
72 <param name="inputFile" value="picard_ARRG.bam" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
73 <param name="rglb" value="tumor-a" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
74 <param name="rgpl" value="Illumina" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
75 <param name="rgpu" value="run-1" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
76 <param name="rgsm" value="sample-a" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
77 <param name="rgid" value="id-1" />
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
78 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
79 </test>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
80 </tests>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
81 <help>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
82
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
83 .. class:: infomark
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
84
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
85 **Purpose**
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
86
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
87 Add or Replace Read Groups in an input BAM or SAM file.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
88
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
89 @dataset_collections@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
90
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
91 @RG@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
92
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
93 @description@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
94
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
95 INPUT=File
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
96 I=File Input file (bam or sam). Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
97
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
98 OUTPUT=File
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
99 O=File Output file (bam or sam). Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
100
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
101 SORT_ORDER=SortOrder
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
102 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
103 Default value: null. Possible values: {unsorted, queryname, coordinate}
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
104
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
105 RGID=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
106 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
107 value.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
108
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
109 RGLB=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
110 LB=String Read Group Library Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
111
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
112 RGPL=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
113 PL=String Read Group platform (e.g. illumina, solid) Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
114
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
115 RGPU=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
116 PU=String Read Group platform unit (eg. run barcode) Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
117
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
118 RGSM=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
119 SM=String Read Group sample name Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
120
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
121 RGCN=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
122 CN=String Read Group sequencing center name Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
123
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
124 RGDS=String
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
125 DS=String Read Group description Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
126
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
127 RGDT=Iso8601Date
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
128 DT=Iso8601Date Read Group run date Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
129
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
130 RGPI=Integer
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
131 PI=Integer Read Group predicted insert size Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
132
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
133 @more_info@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
134 </help>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
135 </tool>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
136
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
137
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
138
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
139
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
140
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
141
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
142
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
143
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
144
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
145
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
146
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
147
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
148