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comparison picard_AddOrReplaceReadGroups.xml @ 8:3a3234d7a2e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:53:10 -0400
parents 3d4f1fa26f0e
children 05087b27692a
comparison
equal deleted inserted replaced
7:379fdf4c41ac 8:3a3234d7a2e8
1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.126.0"> 1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0">
2 <description>add or replaces read group information</description> 2 <description>add or replaces read group information</description>
3 <requirements>
4 <requirement type="package" version="1.126.0">picard</requirement>
5 </requirements>
6
7 <macros> 3 <macros>
8 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <import>read_group_macros.xml</import>
9 </macros> 6 </macros>
10 7 <expand macro="requirements" />
11 <command> 8 <command>
9 @define_read_group_helpers@
10 #set $rg_auto_name = $read_group_name_default($inputFile)
11 @set_read_group_vars@
12 @java_options@ 12 @java_options@
13 java -jar \$JAVA_JAR_PATH/picard.jar 13 java -jar \$JAVA_JAR_PATH/picard.jar
14 AddOrReplaceReadGroups 14 AddOrReplaceReadGroups
15 INPUT="${inputFile}" 15 INPUT="${inputFile}"
16 RGLB="${rglb}" 16 $format_read_group("RGLB=", $rg_lb, '"')
17 RGPL="${rgpl}" 17 $format_read_group("RGPL=", $rg_pl, '"')
18 RGPU="${rgpu}" 18 $format_read_group("RGPU=", $rg_pu, '"')
19 RGSM="${rgsm}" 19 $format_read_group("RGSM=", $rg_sm, '"')
20 RGID="${rgid}" 20 $format_read_group("RGID=", $rg_id, '"')
21 21 $format_read_group("RGDS=", $rg_ds, '"')
22 #if str( $rgcn): 22 $format_read_group("RGPI=", $rg_pi, '"')
23 RGCN="${rgcn}" 23 $format_read_group("RGDT=", $rg_dt, '"')
24 #end if
25
26 #if str( $rgds):
27 RGDS="${rgds}"
28 #end if
29
30 #if str( $rgpi):
31 RGPI="${rgpi}"
32 #end if
33
34 #if str( $rgdt):
35 RGDT="${rgdt}"
36 #end if
37
38 VALIDATION_STRINGENCY="${validation_stringency}" 24 VALIDATION_STRINGENCY="${validation_stringency}"
39 QUIET=true 25 QUIET=true
40 VERBOSITY=ERROR 26 VERBOSITY=ERROR
41 OUTPUT="${outFile}" 27 OUTPUT="${outFile}"
42 28
43 </command> 29 </command>
44 30
45 <inputs> 31 <inputs>
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" /> 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" />
47 <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" /> 33 <expand macro="read_group_inputs_picard" />
48 <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" />
49 <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" />
50 <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" />
51 <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" />
52 <!-- optional params -->
53 <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" />
54 <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" />
55 <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" />
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)"/>
57
58 <expand macro="VS" /> 34 <expand macro="VS" />
59 35
60 </inputs> 36 </inputs>
61 37
62 <outputs> 38 <outputs>
68 </stdio> 44 </stdio>
69 45
70 <tests> 46 <tests>
71 <test> 47 <test>
72 <param name="inputFile" value="picard_ARRG.bam" /> 48 <param name="inputFile" value="picard_ARRG.bam" />
73 <param name="rglb" value="tumor-a" /> 49 <param name="LB" value="tumor-a" />
74 <param name="rgpl" value="Illumina" /> 50 <param name="PL" value="ILLUMINA" />
75 <param name="rgpu" value="run-1" /> 51 <param name="PU" value="run-1" />
76 <param name="rgsm" value="sample-a" /> 52 <param name="SM" value="sample-a" />
77 <param name="rgid" value="id-1" /> 53 <param name="ID" value="id-1" />
78 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" /> 54 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
79 </test> 55 </test>
80 </tests> 56 </tests>
81 <help> 57 <help>
82 58
144 120
145 121
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