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1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.126.0">
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2 <description>add or replaces read group information</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13 java -jar \$JAVA_JAR_PATH/picard.jar
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14 AddOrReplaceReadGroups
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15 INPUT="${inputFile}"
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16 RGLB="${rglb}"
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17 RGPL="${rgpl}"
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18 RGPU="${rgpu}"
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19 RGSM="${rgsm}"
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20 RGID="${rgid}"
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21
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22 #if str( $rgcn):
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23 RGCN="${rgcn}"
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0
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24 #end if
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25
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26 #if str( $rgds):
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27 RGDS="${rgds}"
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28 #end if
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29
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30 #if str( $rgpi):
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31 RGPI="${rgpi}"
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32 #end if
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33
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34 #if str( $rgdt):
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35 RGDT="${rgdt}"
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36 #end if
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37
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38 VALIDATION_STRINGENCY="${validation_stringency}"
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39 QUIET=true
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40 VERBOSITY=ERROR
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41 OUTPUT="${outFile}"
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42
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43 </command>
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44
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45 <inputs>
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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" />
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47 <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" />
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48 <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" />
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49 <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" />
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50 <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" />
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51 <param name="rgpu" value="run-1" type="text" label="Read Group Platform Unit" help="RGPU; Required; e.g., run, barcode, etc" />
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52 <!-- optional params -->
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53 <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" />
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54 <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" />
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55 <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" />
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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)"/>
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57
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58 <expand macro="VS" />
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59
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0
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60 </inputs>
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61
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62 <outputs>
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63 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
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64 </outputs>
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65
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66 <stdio>
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67 <exit_code range="1:" level="fatal"/>
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68 </stdio>
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69
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70 <tests>
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71 <test>
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72 <param name="inputFile" value="picard_ARRG.bam" />
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73 <param name="rglb" value="tumor-a" />
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74 <param name="rgpl" value="Illumina" />
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75 <param name="rgpu" value="run-1" />
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76 <param name="rgsm" value="sample-a" />
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77 <param name="rgid" value="id-1" />
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78 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
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79 </test>
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80 </tests>
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81 <help>
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82
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83 .. class:: infomark
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84
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85 **Purpose**
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86
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87 Add or Replace Read Groups in an input BAM or SAM file.
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88
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89 @dataset_collections@
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90
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91 @RG@
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92
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93 @description@
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94
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95 INPUT=File
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96 I=File Input file (bam or sam). Required.
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97
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98 OUTPUT=File
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99 O=File Output file (bam or sam). Required.
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100
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101 SORT_ORDER=SortOrder
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102 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
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103 Default value: null. Possible values: {unsorted, queryname, coordinate}
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104
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105 RGID=String
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106 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
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107 value.
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108
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109 RGLB=String
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110 LB=String Read Group Library Required.
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111
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112 RGPL=String
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113 PL=String Read Group platform (e.g. illumina, solid) Required.
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114
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115 RGPU=String
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116 PU=String Read Group platform unit (eg. run barcode) Required.
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117
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118 RGSM=String
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119 SM=String Read Group sample name Required.
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120
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121 RGCN=String
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122 CN=String Read Group sequencing center name Default value: null.
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123
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124 RGDS=String
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125 DS=String Read Group description Default value: null.
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126
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127 RGDT=Iso8601Date
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128 DT=Iso8601Date Read Group run date Default value: null.
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129
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130 RGPI=Integer
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131 PI=Integer Read Group predicted insert size Default value: null.
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132
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133 @more_info@
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134 </help>
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135 </tool>
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