Mercurial > repos > iuc > rgrnastar

annotate macros.xml @ 16:e132e7d02a3e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
author iuc
date Fri, 04 Dec 2020 22:05:07 +0000
parents 5ec75f5dae3c
children 7ed2edc1337f
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318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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1 <macros>
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2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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3 whenever you make changes to the following two version tokens!
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4 The data manager uses a symlink to this macro file to keep the STAR and
b9e04854e2bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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5 the index versions in sync, but you should manually adjust the +galaxy
b9e04854e2bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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6 version number. -->
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7 <!-- STAR version to be used -->
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8 <token name="@VERSION@">2.7.6a</token>
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9 <!-- STAR index version compatible with this version of STAR
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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10 This is the STAR version that introduced the index structure expected
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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11 by the current version.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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12 It can be found for any specific version of STAR with:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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13 STAR -h | grep versionGenome
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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14 or by looking for the versionGenome parameter in source/parametersDefault
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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15 of STAR's source code -->
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16 <token name="@IDX_VERSION@">2.7.4a</token>
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17 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
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18
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19 <xml name="requirements">
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20 <requirements>
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21 <requirement type="package" version="@VERSION@">star</requirement>
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22 <requirement type="package" version="1.9">samtools</requirement>
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23 <yield />
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24 </requirements>
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25 </xml>
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26
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27 <xml name="edam">
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28 <edam_topics>
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29 <edam_topic>topic_3170</edam_topic>
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30 <edam_topic>topic_3308</edam_topic>
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31 </edam_topics>
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32 <edam_operations>
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33 <edam_operation>operation_0292</edam_operation>
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34 </edam_operations>
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35 </xml>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
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36
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37 <xml name="index_selection" token_with_gene_model="0">
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38 <param argument="--genomeDir" name="genomeDir" type="select"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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39 label="Select reference genome"
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40 help="If your genome of interest is not listed, contact the Galaxy team">
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41 <options from_data_table="@IDX_DATA_TABLE@">
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42 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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43 <filter type="static_value" column="5" value="@IDX_VERSION@" />
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44 <filter type="sort_by" column="2" />
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45 <validator type="no_options" message="No indexes are available for the selected input dataset" />
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46 </options>
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47 </param>
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48 </xml>
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49
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50 <token name="@FASTQ_GZ_OPTION@">
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51 --readFilesCommand zcat
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52 </token>
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53 <xml name="citations">
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54 <citations>
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55 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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56 </citations>
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57 </xml>
10
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58 <xml name="@SJDBOPTIONS@" token_optional="true">
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59 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
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60 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
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61 </xml>
8
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62 <xml name="dbKeyActions">
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63 <actions>
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64 <conditional name="refGenomeSource.geneSource">
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65 <when value="indexed">
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66 <action type="metadata" name="dbkey">
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67 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
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68 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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69 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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70 </option>
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71 </action>
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72 </when>
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73 <when value="history">
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74 <action type="metadata" name="dbkey">
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75 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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76 </action>
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77 </when>
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78 </conditional>
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79 </actions>
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80 </xml>
10
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81 <token name="@TEMPINDEX@"><![CDATA[
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82 ## Create temporary index for custom reference
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83 #if str($refGenomeSource.geneSource) == 'history':
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84 mkdir -p tempstargenomedir &&
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85 STAR
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86 --runMode genomeGenerate
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87 --genomeDir 'tempstargenomedir'
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88 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
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89 ## Handle difference between indices with/without annotations
15
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90 #if 'GTFconditional' in $refGenomeSource:
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91 ## GTFconditional exists only in STAR, but not STARsolo
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92 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
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93 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
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94 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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95 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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96 --sjdbGTFtagExonParentTranscript Parent
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97 #end if
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98 #end if
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99 #else:
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100 ## ref genome selection is less complex for STARsolo cause
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101 ## with-gtf is mandatory there
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102 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
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103 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
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104 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
10
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105 --sjdbGTFtagExonParentTranscript Parent
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106 #end if
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107 #end if
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108 #if str($refGenomeSource.genomeSAindexNbases):
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109 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
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110 #end if
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111 --runThreadN \${GALAXY_SLOTS:-4}
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112 &&
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113 #end if
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114 ]]></token>
12
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115 <token name="@REFGENOMEHANDLING@" ><![CDATA[
10
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116 --runThreadN \${GALAXY_SLOTS:-4}
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117 --genomeLoad NoSharedMemory
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118 --genomeDir
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119 #if str($refGenomeSource.geneSource) == 'history':
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120 tempstargenomedir
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121 #else:
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122 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
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123 ## Handle difference between indices with/without annotations
12
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124 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
10
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125 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
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126 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
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127 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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128 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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129 --sjdbGTFtagExonParentTranscript Parent
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130 #end if
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131 #end if
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132 #end if
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133 #end if
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134 ]]></token>
15
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135 <xml name="ref_selection">
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136 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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137 <!-- Currently, this parameter is not exposed in the wrapper,
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138 but used only in the tests to avoid excessive index sizes for
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139 the tiny test genomes. -->
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140 <param name="genomeSAindexNbases" type="hidden" value="" />
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141 </xml>
10
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142 <xml name="stdio" >
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143 <stdio>
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144 <regex match="FATAL error" source="both" level="fatal"/>
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145 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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146 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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147 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
12
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148 <yield />
10
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149 </stdio>
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150 </xml>
3
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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151 </macros>