Mercurial > repos > devteam > picard

annotate picard_AddOrReplaceReadGroups.xml @ 32:f9242e01365a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 2a17c789e0a5
children 3f254c5ced1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 15
diff changeset
1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
2 <description>add or replaces read group information</description>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
4 <import>picard_macros.xml</import>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
5 <import>read_group_macros.xml</import>
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
6 <token name="@WRAPPER_VERSION@">1</token>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
7 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
8 <expand macro="requirements" />
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
10 @define_read_group_helpers@
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
11 #set $rg_auto_name = $read_group_name_default($inputFile)
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
12 @set_read_group_vars@
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
13 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
14 @symlink_element_identifier@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
15 picard
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
16 AddOrReplaceReadGroups
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
17 INPUT='$escaped_element_identifier'
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
18 $format_read_group("RGLB=", $rg_lb, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
19 $format_read_group("RGPL=", $rg_pl, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
20 $format_read_group("RGPU=", $rg_pu, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
21 $format_read_group("RGSM=", $rg_sm, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
22 $format_read_group("RGID=", $rg_id, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
23 $format_read_group("RGDS=", $rg_ds, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
24 $format_read_group("RGPI=", $rg_pi, '"')
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
25 $format_read_group("RGDT=", $rg_dt, '"')
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
26 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
27 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
28 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
29 OUTPUT="${outFile}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
30
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
31 ]]></command>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
32
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
33 <inputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
34 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
35 <expand macro="read_group_inputs_picard" />
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
36 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
37
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
38 </inputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
39
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
40 <outputs>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
41 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
42 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
43
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
44
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
45 <tests>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
46 <test>
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
47 <param name="inputFile" value="picard_ARRG.bam" />
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
48 <param name="LB" value="tumor-a" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
49 <param name="PL" value="ILLUMINA" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
50 <param name="PU" value="run-1" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
51 <param name="SM" value="sample-a" />
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
52 <param name="ID" value="id-1" />
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
53 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
54 </test>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
55 </tests>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
56 <help>
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
57
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
58 .. class:: infomark
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
59
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
60 **Purpose**
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
61
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
62 Add or Replace Read Groups in an input BAM or SAM file.
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
63
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
64 @dataset_collections@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
65
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
66 @RG@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
67
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
68 @description@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
69
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
70 INPUT=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
71 I=File Input file (bam or sam). Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
72
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
73 OUTPUT=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
74 O=File Output file (bam or sam). Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
75
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
76 SORT_ORDER=SortOrder
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
77 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
78 Default value: null. Possible values: {unsorted, queryname, coordinate}
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
79
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
80 RGID=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
81 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
82 value.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
83
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
84 RGLB=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
85 LB=String Read Group Library Required.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
86
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
87 RGPL=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
88 PL=String Read Group platform (e.g. illumina, solid) Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
89
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
90 RGPU=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
91 PU=String Read Group platform unit (eg. run barcode) Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
92
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
93 RGSM=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
94 SM=String Read Group sample name Required.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
95
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
96 RGCN=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
97 CN=String Read Group sequencing center name Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
98
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
99 RGDS=String
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
100 DS=String Read Group description Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
101
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
102 RGDT=Iso8601Date
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
103 DT=Iso8601Date Read Group run date Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
104
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
105 RGPI=Integer
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
106 PI=Integer Read Group predicted insert size Default value: null.
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
107
5
3d4f1fa26f0e Uploaded
devteam
parents: 2
diff changeset
108 @more_info@
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
109 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 15
diff changeset
110 <expand macro="citations" />
0
1cd7f3b42609 Uploaded tool.
devteam
parents:
diff changeset
111 </tool>