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1 <tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.122.0">
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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="1.122.0">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/AddOrReplaceReadGroups.jar
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14 INPUT="${inputFile}"
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15 RGLB="${rglb}"
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16 RGPL="${rgpl}"
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17 RGPU="${rgpu}"
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18 RGSM="${rgsm}"
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19 RGID="${rgid}"
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20
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21 #if str( $rgcn):
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22 RGCN="${rgcn}"
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23 #end if
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24
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25 #if str( $rgds):
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26 RGDS="${rgds}"
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27 #end if
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28
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29 #if str( $rgpi):
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30 RGPI="${rgpi}"
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31 #end if
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32
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33 #if str( $rgdt):
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34 RGDT="${rgdt}"
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35 #end if
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36
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37 VALIDATION_STRINGENCY="${validation_stringency}"
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38 QUIET=true
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39 VERBOSITY=ERROR
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40 OUTPUT="${outFile}"
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41
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42 </command>
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43
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44 <inputs>
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45 <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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46 <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" />
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47 <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" />
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48 <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" />
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49 <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" />
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50 <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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51 <!-- optional params -->
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52 <param name="rgcn" value="" optional="True" type="text" label="Read Group sequencing center name" help="RGCN; Optional" />
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53 <param name="rgds" value="" optional="True" type="text" label="Read Group description" help="RGDS; Optional" />
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54 <param name="rgpi" value="" optional="True" type="integer" label="Read Group predicted insert size" help="RGPI; Optional" />
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55 <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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56
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57 <expand macro="VS" />
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58
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59 </inputs>
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60
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61 <outputs>
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62 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
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63 </outputs>
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64
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65 <stdio>
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66 <exit_code range="1:" level="fatal"/>
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67 </stdio>
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68
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69 <tests>
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70 <test>
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71 <param name="inputFile" value="picard_ARRG.bam" />
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72 <param name="rglb" value="tumor-a" />
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73 <param name="rgpl" value="Illumina" />
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74 <param name="rgpu" value="run-1" />
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75 <param name="rgsm" value="sample-a" />
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76 <param name="rgid" value="id-1" />
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77 <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
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78 </test>
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79 </tests>
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80 <help>
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81
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82 .. class:: infomark
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83
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84 **Purpose**
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85
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86 Add or Replace Read Groups in an input BAM or SAM file.
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87
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88 @dataset_collections@
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89
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90 @RG@
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91
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92 @description@
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93
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94 INPUT=File
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95 I=File Input file (bam or sam). Required.
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96
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97 OUTPUT=File
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98 O=File Output file (bam or sam). Required.
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99
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100 SORT_ORDER=SortOrder
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101 SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
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102 Default value: null. Possible values: {unsorted, queryname, coordinate}
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103
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104 RGID=String
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105 ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default
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106 value.
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107
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108 RGLB=String
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109 LB=String Read Group Library Required.
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110
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111 RGPL=String
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112 PL=String Read Group platform (e.g. illumina, solid) Required.
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113
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114 RGPU=String
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115 PU=String Read Group platform unit (eg. run barcode) Required.
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116
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117 RGSM=String
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118 SM=String Read Group sample name Required.
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119
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120 RGCN=String
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121 CN=String Read Group sequencing center name Default value: null.
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122
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123 RGDS=String
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124 DS=String Read Group description Default value: null.
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125
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126 RGDT=Iso8601Date
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127 DT=Iso8601Date Read Group run date Default value: null.
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128
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129 RGPI=Integer
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130 PI=Integer Read Group predicted insert size Default value: null.
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131
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132 @more_info@
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133 </help>
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134 </tool>
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135
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