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comparison picard_AddOrReplaceReadGroups.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>add or replaces read group information</description> 2 <description>add or replaces read group information</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
6 <token name="@WRAPPER_VERSION@">1</token> 6 <token name="@WRAPPER_VERSION@">0</token>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @define_read_group_helpers@ 10 @define_read_group_helpers@
11 #set $rg_auto_name = $read_group_name_default($inputFile) 11 #set $rg_auto_name = $read_group_name_default($inputFile)
12 @set_read_group_vars@ 12 @set_read_group_vars@
13 @java_options@ 13 @java_options@
14 @symlink_element_identifier@ 14 @symlink_element_identifier@
15 picard 15 picard AddOrReplaceReadGroups
16 AddOrReplaceReadGroups 16 --INPUT '$escaped_element_identifier'
17 INPUT='$escaped_element_identifier' 17 $format_read_group("", $rg_lb, quote='"', arg=" --RGLB ")
18 $format_read_group("RGLB=", $rg_lb, '"') 18 $format_read_group("", $rg_pl, quote='"', arg=" --RGPL ")
19 $format_read_group("RGPL=", $rg_pl, '"') 19 $format_read_group("", $rg_pu, quote='"', arg=" --RGPU ")
20 $format_read_group("RGPU=", $rg_pu, '"') 20 $format_read_group("", $rg_sm, quote='"', arg=" --RGSM ")
21 $format_read_group("RGSM=", $rg_sm, '"') 21 $format_read_group("", $rg_id, quote='"', arg=" --RGID ")
22 $format_read_group("RGID=", $rg_id, '"') 22 $format_read_group("", $rg_ds, quote='"', arg=" --RGDS ")
23 $format_read_group("RGDS=", $rg_ds, '"') 23 $format_read_group("", $rg_pi, quote='"', arg=" --RGPI ")
24 $format_read_group("RGPI=", $rg_pi, '"') 24 $format_read_group("", $rg_dt, quote='"', arg=" --RGDT ")
25 $format_read_group("RGDT=", $rg_dt, '"') 25 --OUTPUT '${outFile}'
26 VALIDATION_STRINGENCY="${validation_stringency}" 26 --VALIDATION_STRINGENCY '${validation_stringency}'
27 QUIET=true 27 --QUIET true
28 VERBOSITY=ERROR 28 --VERBOSITY ERROR
29 OUTPUT="${outFile}"
30 29
31 ]]></command> 30 ]]></command>
32 31 <inputs>
33 <inputs> 32 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
34 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 33 <expand macro="read_group_inputs_picard"/>
35 <expand macro="read_group_inputs_picard" /> 34 <expand macro="VS"/>
36 <expand macro="VS" /> 35 </inputs>
37 36 <outputs>
38 </inputs> 37 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
39 38 </outputs>
40 <outputs> 39 <tests>
41 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/> 40 <test>
42 </outputs> 41 <param name="inputFile" value="picard_ARRG.bam"/>
43 42 <param name="LB" value="tumor-a"/>
44 43 <param name="PL" value="ILLUMINA"/>
45 <tests> 44 <param name="PU" value="run-1"/>
46 <test> 45 <param name="SM" value="sample-a"/>
47 <param name="inputFile" value="picard_ARRG.bam" /> 46 <param name="ID" value="id-1"/>
48 <param name="LB" value="tumor-a" /> 47 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam"/>
49 <param name="PL" value="ILLUMINA" /> 48 </test>
50 <param name="PU" value="run-1" /> 49 </tests>
51 <param name="SM" value="sample-a" /> 50 <help>
52 <param name="ID" value="id-1" />
53 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
54 </test>
55 </tests>
56 <help>
57 51
58 .. class:: infomark 52 .. class:: infomark
59 53
60 **Purpose** 54 **Purpose**
61 55
105 RGPI=Integer 99 RGPI=Integer
106 PI=Integer Read Group predicted insert size Default value: null. 100 PI=Integer Read Group predicted insert size Default value: null.
107 101
108 @more_info@ 102 @more_info@
109 </help> 103 </help>
110 <expand macro="citations" /> 104 <expand macro="citations"/>
111 </tool> 105 </tool>