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comparison picard_AddOrReplaceReadGroups.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
comparison
equal deleted inserted replaced
12:05087b27692a 13:7e6fd3d0f16e
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 @define_read_group_helpers@ 9 @define_read_group_helpers@
10 #set $rg_auto_name = $read_group_name_default($inputFile) 10 #set $rg_auto_name = $read_group_name_default($inputFile)
11 @set_read_group_vars@ 11 @set_read_group_vars@
12 @java_options@ 12 @java_options@
13 @symlink_element_identifier@
13 picard 14 picard
14 AddOrReplaceReadGroups 15 AddOrReplaceReadGroups
15 INPUT="${inputFile}" 16 INPUT='$inputFile.element_identifier'
16 $format_read_group("RGLB=", $rg_lb, '"') 17 $format_read_group("RGLB=", $rg_lb, '"')
17 $format_read_group("RGPL=", $rg_pl, '"') 18 $format_read_group("RGPL=", $rg_pl, '"')
18 $format_read_group("RGPU=", $rg_pu, '"') 19 $format_read_group("RGPU=", $rg_pu, '"')
19 $format_read_group("RGSM=", $rg_sm, '"') 20 $format_read_group("RGSM=", $rg_sm, '"')
20 $format_read_group("RGID=", $rg_id, '"') 21 $format_read_group("RGID=", $rg_id, '"')
23 $format_read_group("RGDT=", $rg_dt, '"') 24 $format_read_group("RGDT=", $rg_dt, '"')
24 VALIDATION_STRINGENCY="${validation_stringency}" 25 VALIDATION_STRINGENCY="${validation_stringency}"
25 QUIET=true 26 QUIET=true
26 VERBOSITY=ERROR 27 VERBOSITY=ERROR
27 OUTPUT="${outFile}" 28 OUTPUT="${outFile}"
28 29
29 </command> 30 </command>
30 31
31 <inputs> 32 <inputs>
32 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 33 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
33 <expand macro="read_group_inputs_picard" /> 34 <expand macro="read_group_inputs_picard" />
34 <expand macro="VS" /> 35 <expand macro="VS" />
35 36
36 </inputs> 37 </inputs>
37 38
38 <outputs> 39 <outputs>
39 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/> 40 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
40 </outputs> 41 </outputs>
41 42
42 43
43 <tests> 44 <tests>
44 <test> 45 <test>
45 <param name="inputFile" value="picard_ARRG.bam" /> 46 <param name="inputFile" value="picard_ARRG.bam" />
46 <param name="LB" value="tumor-a" /> 47 <param name="LB" value="tumor-a" />
47 <param name="PL" value="ILLUMINA" /> 48 <param name="PL" value="ILLUMINA" />
64 @RG@ 65 @RG@
65 66
66 @description@ 67 @description@
67 68
68 INPUT=File 69 INPUT=File
69 I=File Input file (bam or sam). Required. 70 I=File Input file (bam or sam). Required.
70 71
71 OUTPUT=File 72 OUTPUT=File
72 O=File Output file (bam or sam). Required. 73 O=File Output file (bam or sam). Required.
73 74
74 SORT_ORDER=SortOrder 75 SORT_ORDER=SortOrder
75 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. 76 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
76 Default value: null. Possible values: {unsorted, queryname, coordinate} 77 Default value: null. Possible values: {unsorted, queryname, coordinate}
77 78
78 RGID=String 79 RGID=String
79 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default 80 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
80 value. 81 value.
81 82
82 RGLB=String 83 RGLB=String
83 LB=String Read Group Library Required. 84 LB=String Read Group Library Required.
84 85
85 RGPL=String 86 RGPL=String
86 PL=String Read Group platform (e.g. illumina, solid) Required. 87 PL=String Read Group platform (e.g. illumina, solid) Required.
87 88
88 RGPU=String 89 RGPU=String
89 PU=String Read Group platform unit (eg. run barcode) Required. 90 PU=String Read Group platform unit (eg. run barcode) Required.
90 91
91 RGSM=String 92 RGSM=String
92 SM=String Read Group sample name Required. 93 SM=String Read Group sample name Required.
93 94
94 RGCN=String 95 RGCN=String
95 CN=String Read Group sequencing center name Default value: null. 96 CN=String Read Group sequencing center name Default value: null.
96 97
97 RGDS=String 98 RGDS=String
98 DS=String Read Group description Default value: null. 99 DS=String Read Group description Default value: null.
99 100
100 RGDT=Iso8601Date 101 RGDT=Iso8601Date
101 DT=Iso8601Date Read Group run date Default value: null. 102 DT=Iso8601Date Read Group run date Default value: null.
102 103
103 RGPI=Integer 104 RGPI=Integer
104 PI=Integer Read Group predicted insert size Default value: null. 105 PI=Integer Read Group predicted insert size Default value: null.
105 106
106 @more_info@ 107 @more_info@
107 </help> 108 </help>
108 </tool> 109 </tool>
109 110