Mercurial > repos > devteam > picard_122_up
comparison picard_AddOrReplaceReadGroups.xml @ 0:b76a4f17bbbb draft
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author | devteam |
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date | Thu, 23 Oct 2014 11:31:30 -0400 |
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-1:000000000000 | 0:b76a4f17bbbb |
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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> | |
135 | |
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