Mercurial > repos > devteam > picard

annotate picard_AddOrReplaceReadGroups.xml @ 20:2a17c789e0a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author iuc
date Tue, 19 Jun 2018 11:28:49 -0400
parents 5053a18d9bc8
children f9242e01365a
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1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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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@">1</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[
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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
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16 AddOrReplaceReadGroups
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17 INPUT='$escaped_element_identifier'
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18 $format_read_group("RGLB=", $rg_lb, '"')
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19 $format_read_group("RGPL=", $rg_pl, '"')
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20 $format_read_group("RGPU=", $rg_pu, '"')
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21 $format_read_group("RGSM=", $rg_sm, '"')
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22 $format_read_group("RGID=", $rg_id, '"')
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23 $format_read_group("RGDS=", $rg_ds, '"')
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24 $format_read_group("RGPI=", $rg_pi, '"')
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25 $format_read_group("RGDT=", $rg_dt, '"')
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26 VALIDATION_STRINGENCY="${validation_stringency}"
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27 QUIET=true
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28 VERBOSITY=ERROR
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29 @TMPDIR_OPTION@
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30 OUTPUT="${outFile}"
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31
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32 ]]></command>
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33
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34 <inputs>
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35 <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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36 <expand macro="read_group_inputs_picard" />
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37 <expand macro="VS" />
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38
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39 </inputs>
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40
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41 <outputs>
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42 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
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43 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="inputFile" value="picard_ARRG.bam" />
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49 <param name="LB" value="tumor-a" />
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50 <param name="PL" value="ILLUMINA" />
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51 <param name="PU" value="run-1" />
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52 <param name="SM" value="sample-a" />
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53 <param name="ID" value="id-1" />
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54 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
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55 </test>
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56 </tests>
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57 <help>
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58
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59 .. class:: infomark
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60
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61 **Purpose**
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62
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63 Add or Replace Read Groups in an input BAM or SAM file.
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64
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65 @dataset_collections@
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66
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67 @RG@
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68
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69 @description@
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70
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71 INPUT=File
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72 I=File Input file (bam or sam). Required.
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73
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74 OUTPUT=File
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75 O=File Output file (bam or sam). Required.
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76
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77 SORT_ORDER=SortOrder
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78 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
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79 Default value: null. Possible values: {unsorted, queryname, coordinate}
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81 RGID=String
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82 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
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83 value.
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84
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85 RGLB=String
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86 LB=String Read Group Library Required.
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87
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88 RGPL=String
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89 PL=String Read Group platform (e.g. illumina, solid) Required.
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91 RGPU=String
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92 PU=String Read Group platform unit (eg. run barcode) Required.
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93
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94 RGSM=String
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95 SM=String Read Group sample name Required.
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96
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97 RGCN=String
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98 CN=String Read Group sequencing center name Default value: null.
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99
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100 RGDS=String
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101 DS=String Read Group description Default value: null.
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102
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103 RGDT=Iso8601Date
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104 DT=Iso8601Date Read Group run date Default value: null.
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105
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106 RGPI=Integer
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107 PI=Integer Read Group predicted insert size Default value: null.
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108
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109 @more_info@
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110 </help>
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111 <expand macro="citations" />
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112 </tool>