Mercurial > repos > devteam > picard

annotate 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
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33
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>add or replaces read group information</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <import>read_group_macros.xml</import>
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6 <token name="@WRAPPER_VERSION@">0</token>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
8
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10 @define_read_group_helpers@
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11 #set $rg_auto_name = $read_group_name_default($inputFile)
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12 @set_read_group_vars@
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13 @java_options@
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14 @symlink_element_identifier@
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15 picard AddOrReplaceReadGroups
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16 --INPUT '$escaped_element_identifier'
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17 $format_read_group("", $rg_lb, quote='"', arg=" --RGLB ")
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18 $format_read_group("", $rg_pl, quote='"', arg=" --RGPL ")
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19 $format_read_group("", $rg_pu, quote='"', arg=" --RGPU ")
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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20 $format_read_group("", $rg_sm, quote='"', arg=" --RGSM ")
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21 $format_read_group("", $rg_id, quote='"', arg=" --RGID ")
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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22 $format_read_group("", $rg_ds, quote='"', arg=" --RGDS ")
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23 $format_read_group("", $rg_pi, quote='"', arg=" --RGPI ")
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24 $format_read_group("", $rg_dt, quote='"', arg=" --RGDT ")
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25 --OUTPUT '${outFile}'
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26 --VALIDATION_STRINGENCY '${validation_stringency}'
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27 --QUIET true
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28 --VERBOSITY ERROR
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29
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30 ]]></command>
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31 <inputs>
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32 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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33 <expand macro="read_group_inputs_picard"/>
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34 <expand macro="VS"/>
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35 </inputs>
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36 <outputs>
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37 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="inputFile" value="picard_ARRG.bam"/>
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42 <param name="LB" value="tumor-a"/>
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43 <param name="PL" value="ILLUMINA"/>
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44 <param name="PU" value="run-1"/>
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45 <param name="SM" value="sample-a"/>
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46 <param name="ID" value="id-1"/>
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47 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam"/>
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48 </test>
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49 </tests>
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50 <help>
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51
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52 .. class:: infomark
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53
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54 **Purpose**
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55
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56 Add or Replace Read Groups in an input BAM or SAM file.
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57
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58 @dataset_collections@
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59
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60 @RG@
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61
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62 @description@
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63
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64 INPUT=File
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65 I=File Input file (bam or sam). Required.
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66
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67 OUTPUT=File
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68 O=File Output file (bam or sam). Required.
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69
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70 SORT_ORDER=SortOrder
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71 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
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72 Default value: null. Possible values: {unsorted, queryname, coordinate}
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73
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74 RGID=String
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75 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
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76 value.
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77
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78 RGLB=String
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79 LB=String Read Group Library Required.
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80
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81 RGPL=String
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82 PL=String Read Group platform (e.g. illumina, solid) Required.
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83
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84 RGPU=String
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85 PU=String Read Group platform unit (eg. run barcode) Required.
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86
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87 RGSM=String
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88 SM=String Read Group sample name Required.
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89
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90 RGCN=String
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91 CN=String Read Group sequencing center name Default value: null.
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92
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93 RGDS=String
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94 DS=String Read Group description Default value: null.
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95
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96 RGDT=Iso8601Date
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97 DT=Iso8601Date Read Group run date Default value: null.
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98
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99 RGPI=Integer
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100 PI=Integer Read Group predicted insert size Default value: null.
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101
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102 @more_info@
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103 </help>
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104 <expand macro="citations"/>
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105 </tool>