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annotate macros.xml @ 0:c4769d5e5c2b draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
author dave
date Thu, 30 Jul 2020 14:36:52 +0000
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c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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1 <macros>
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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3 whenever you make changes to the following two version tokens!
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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4 The data manager uses a symlink to this macro file to keep the STAR and
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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5 the index versions in sync, but you should manually adjust the +galaxy
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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6 version number. -->
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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7 <!-- STAR version to be used -->
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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8 <token name="@VERSION@">2.7.5a</token>
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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9 <!-- STAR index version compatible with this version of STAR
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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10 This is the STAR version that introduced the index structure expected
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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11 by the current version.
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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12 It can be found for any specific version of STAR with:
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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13 STAR -h | grep versionGenome
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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14 or by looking for the versionGenome parameter in source/parametersDefault
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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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="index_selection" token_with_gene_model="0">
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28 <param argument="--genomeDir" name="genomeDir" type="select"
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29 label="Select reference genome"
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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30 help="If your genome of interest is not listed, contact the Galaxy team">
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31 <options from_data_table="@IDX_DATA_TABLE@">
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32 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
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33 <filter type="static_value" column="5" value="@IDX_VERSION@" />
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34 <filter type="sort_by" column="2" />
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35 <validator type="no_options" message="No indexes are available for the selected input dataset" />
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36 </options>
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37 </param>
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38 </xml>
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39
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40 <token name="@FASTQ_GZ_OPTION@">
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41 --readFilesCommand zcat
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42 </token>
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43 <xml name="citations">
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44 <citations>
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45 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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46 </citations>
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47 </xml>
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48 <xml name="@SJDBOPTIONS@" token_optional="true">
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49 <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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50 <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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51 </xml>
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52 <xml name="dbKeyActions">
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53 <actions>
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54 <conditional name="refGenomeSource.geneSource">
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55 <when value="indexed">
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56 <action type="metadata" name="dbkey">
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57 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
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58 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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59 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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60 </option>
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61 </action>
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62 </when>
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63 <when value="history">
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64 <action type="metadata" name="dbkey">
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65 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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66 </action>
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67 </when>
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68 </conditional>
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69 </actions>
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70 </xml>
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71 <token name="@TEMPINDEX@"><![CDATA[
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72 ## Create temporary index for custom reference
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73 #if str($refGenomeSource.geneSource) == 'history':
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74 mkdir -p tempstargenomedir &&
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75 STAR
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76 --runMode genomeGenerate
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77 --genomeDir 'tempstargenomedir'
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78 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
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79 ## Handle difference between indices with/without annotations
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80 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
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81 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
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82 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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83 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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84 --sjdbGTFtagExonParentTranscript Parent
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85 #end if
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86 #end if
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87 #if str($refGenomeSource.genomeSAindexNbases):
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88 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
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89 #end if
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90 --runThreadN \${GALAXY_SLOTS:-4}
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91 &&
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92 #end if
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93 ]]></token>
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94 <token name="@REFGENOMEHANDLING@" ><![CDATA[
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95 --runThreadN \${GALAXY_SLOTS:-4}
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96 --genomeLoad NoSharedMemory
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97 --genomeDir
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98 #if str($refGenomeSource.geneSource) == 'history':
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99 tempstargenomedir
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100 #else:
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101 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
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102 ## Handle difference between indices with/without annotations
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103 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
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104 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
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105 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
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106 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
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107 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
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108 --sjdbGTFtagExonParentTranscript Parent
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109 #end if
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110 #end if
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111 #end if
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112 #end if
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113 ]]></token>
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114 <xml name="stdio" >
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115 <stdio>
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116 <regex match="FATAL error" source="both" level="fatal"/>
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117 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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118 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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119 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
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120 <yield />
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121 </stdio>
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122 </xml>
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123 <xml name="refgenomehandling" >
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124 <conditional name="refGenomeSource">
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125 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
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126 <option value="indexed" selected="true">Use a built-in index</option>
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127 <option value="history">Use reference genome from history and create temporary index</option>
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128 </param>
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129 <when value="indexed">
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130 <conditional name="GTFconditional">
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131 <param name="GTFselect" type="select"
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132 label="Reference genome with or without an annotation"
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133 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
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134 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
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135 <option value="with-gtf">use genome reference with builtin gene-model</option>
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136 </param>
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137 <when value="with-gtf">
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138 <expand macro="index_selection" with_gene_model="1" />
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139 </when>
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140 <when value="without-gtf">
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141 <expand macro="index_selection" with_gene_model="0" />
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142 <expand macro="@SJDBOPTIONS@" />
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143 </when>
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144 </conditional>
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145 </when>
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146 <when value="history">
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147 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
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148 <!-- Currently, this parameter is not exposed in the wrapper,
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149 but used only in the tests to avoid excessive index sizes for
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150 the tiny test genomes. -->
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151 <param name="genomeSAindexNbases" type="hidden" value="" />
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152 <conditional name="GTFconditional">
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153 <param name="GTFselect" type="select"
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154 label="Build index with our without known splice junctions annotation"
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155 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
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156 <option value="without-gtf">build index without gene-model</option>
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157 <option value="with-gtf">build index with gene-model</option>
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158 </param>
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159 <when value="with-gtf">
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160 <expand macro="@SJDBOPTIONS@" optional="false"/>
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161 </when>
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162 <when value="without-gtf" />
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
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parents:
diff changeset
163 </conditional>
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
parents:
diff changeset
164 </when>
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
parents:
diff changeset
165 </conditional>
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
parents:
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166 </xml>
c4769d5e5c2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty"
dave
parents:
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167 </macros>