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annotate picard_AddOrReplaceReadGroups.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
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1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.0">
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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 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 @define_read_group_helpers@
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10 #set $rg_auto_name = $read_group_name_default($inputFile)
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11 @set_read_group_vars@
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12 @java_options@
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13 picard
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14 AddOrReplaceReadGroups
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15 INPUT="${inputFile}"
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16 $format_read_group("RGLB=", $rg_lb, '"')
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17 $format_read_group("RGPL=", $rg_pl, '"')
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18 $format_read_group("RGPU=", $rg_pu, '"')
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19 $format_read_group("RGSM=", $rg_sm, '"')
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20 $format_read_group("RGID=", $rg_id, '"')
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21 $format_read_group("RGDS=", $rg_ds, '"')
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22 $format_read_group("RGPI=", $rg_pi, '"')
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23 $format_read_group("RGDT=", $rg_dt, '"')
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24 VALIDATION_STRINGENCY="${validation_stringency}"
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25 QUIET=true
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26 VERBOSITY=ERROR
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27 OUTPUT="${outFile}"
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28
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29 </command>
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30
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31 <inputs>
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32 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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33 <expand macro="read_group_inputs_picard" />
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34 <expand macro="VS" />
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35
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36 </inputs>
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37
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38 <outputs>
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39 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
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40 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="inputFile" value="picard_ARRG.bam" />
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46 <param name="LB" value="tumor-a" />
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47 <param name="PL" value="ILLUMINA" />
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48 <param name="PU" value="run-1" />
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49 <param name="SM" value="sample-a" />
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50 <param name="ID" value="id-1" />
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51 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
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52 </test>
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53 </tests>
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54 <help>
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55
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56 .. class:: infomark
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57
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58 **Purpose**
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59
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60 Add or Replace Read Groups in an input BAM or SAM file.
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61
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62 @dataset_collections@
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63
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64 @RG@
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65
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66 @description@
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67
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68 INPUT=File
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69 I=File Input file (bam or sam). Required.
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70
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71 OUTPUT=File
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72 O=File Output file (bam or sam). Required.
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73
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74 SORT_ORDER=SortOrder
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75 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
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76 Default value: null. Possible values: {unsorted, queryname, coordinate}
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77
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78 RGID=String
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79 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
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80 value.
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81
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82 RGLB=String
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83 LB=String Read Group Library Required.
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84
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85 RGPL=String
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86 PL=String Read Group platform (e.g. illumina, solid) Required.
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87
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88 RGPU=String
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89 PU=String Read Group platform unit (eg. run barcode) Required.
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90
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91 RGSM=String
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92 SM=String Read Group sample name Required.
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93
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94 RGCN=String
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95 CN=String Read Group sequencing center name Default value: null.
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96
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97 RGDS=String
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98 DS=String Read Group description Default value: null.
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99
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100 RGDT=Iso8601Date
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101 DT=Iso8601Date Read Group run date Default value: null.
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102
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103 RGPI=Integer
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104 PI=Integer Read Group predicted insert size Default value: null.
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