Mercurial > repos > gga > tripal_analysis_load_gff3

annotate analysis_load_gff3.xml @ 2:16acaa0aa58c draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:48:01 -0400
parents 5ce8ae1288c1
children c2c58d775e6d
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1 <?xml version="1.0"?>
2
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2 <tool id="analysis_load_gff3" profile="16.04" name="Load a GFF3 annotation file" version="@WRAPPER_VERSION@.1">
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3 <description>into Tripal</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="tripal.py"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
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12
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13 &&
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15 cp '${gff3}' "\${tmp_dir}/annotation.gff3"
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17 &&
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19 @AUTH@
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21 tripaille analysis load_gff3
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23 --organism_id '${organism}'
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25 --analysis_id '${analysis}'
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27 --import_mode '${import_mode}'
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29 #if str($naming.mode) == 'manual':
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30 --re_mrna '${naming.re_mrna}'
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31 --re_protein '${naming.re_protein}'
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32 #end if
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33
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34 #if str($advanced.landmark_type):
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35 --landmark_type '${advanced.landmark_type}'
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36 #end if
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38 #if str($advanced.alt_id_attr):
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39 --alt_id_attr '${advanced.alt_id_attr}'
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40 #end if
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42 ${advanced.create_organism}
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44 #if str($target.target_organism):
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45 --target_organism '${target.target_organism}'
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46 #end if
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48 #if str($target.target_type):
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49 --target_type '${target.target_type}'
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50 #end if
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51
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52 ${target.target_create}
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53
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54 "\${tmp_dir}/annotation.gff3"
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55
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56 &&
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57
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58 echo "Data loaded" > $results
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59 ]]></command>
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60 <inputs>
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61 <param name="gff3"
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62 type="data"
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63 format="gff3"
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64 label="Annotation file" />
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65
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66 <param argument="--organism"
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67 type="select"
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68 dynamic_options="list_organisms()"
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69 label="Organism" />
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70
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71 <param argument="--analysis"
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72 type="select"
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73 dynamic_options="list_analyses()"
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74 label="Analysis" />
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75
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76 <param name="import_mode"
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77 argument="--import_mode"
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78 type="select"
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79 label="Loading method">
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80 <option value="update" selected="true">Import everything, update when already existing</option>
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81 <option value="add_only">Import only new features</option>
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82 </param>
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83
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84 <conditional name="naming">
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85 <param name="mode"
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86 type="select"
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87 label="Naming method for proteins"
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88 help="in case your GFF file does not contain polypeptide features">
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89 <option value="auto">Automatic</option>
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90 <option value="manual">Manual</option>
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91 </param>
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diff changeset
92 <when value="auto"/>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
93 <when value="manual">
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
94 <param name="re_mrna"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
95 argument="--re_mrna"
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diff changeset
96 type="text"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
97 label="Regular expression for the mRNA name"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
98 help="this regex will be used to extract parts of the mRNA feature name">
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
99 <expand macro="sanitized"/>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
100 </param>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
101
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
102 <param name="re_protein"
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103 argument="--re_protein"
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104 type="text"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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105 label="Replacement string for the protein name"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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106 help="will be used to generate the protein name based on the mRNA name">
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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107 <expand macro="sanitized"/>
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108 </param>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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109 </when>
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110 </conditional>
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111
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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112 <section name="advanced" title="Advanced options" expanded="False">
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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113 <param name="landmark_type"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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114 argument="--landmark_type"
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115 type="text"
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116 optional="true"
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117 label="Landmark type"
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118 help="A Sequence Ontology type for the landmark sequences in the GFF fie (e.g. \'chromosome\'). Will be used to create them if they don't already exist." />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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119
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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120 <param name="alt_id_attr"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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121 argument="--alt_id_attr"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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122 type="text"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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123 optional="true"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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124 label="ID attribute"
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125 help="Name of the GFF attribute that contains a unique identifier for each feature. Leave empty to use the 'ID' attribute" />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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126
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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127 <param name="create_organism"
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128 argument="--create_organism"
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129 type="boolean"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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130 checked="false"
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131 truevalue="--create_organism"
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132 falsevalue=""
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133 label="Create organisms specified in 'organism' attribute"
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134 help="If not found, create features referenced in the target attribute." />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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135 </section>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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136
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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137 <section name="target" title="Target attribute handling" expanded="False">
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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138 <param name="target_organism"
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139 argument="--target_organism"
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140 type="text"
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141 optional="true"
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142 label="Target organism name"
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143 help="Name of organism corresponding to target attribute. Abbreviation or common name as created with the 'Create Organism' tool." />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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144 <param name="target_type"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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145 argument="--target_type"
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146 type="text"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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147 optional="true"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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148 label="Target feature type"
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149 help="Type of features referenced in the target attribute. Should be a Sequence Ontology term." />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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150 <param name="target_create"
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151 argument="--target_create"
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152 type="boolean"
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153 checked="false"
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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154 truevalue="--target_create"
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155 falsevalue=""
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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156 label="Create target features"
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157 help="If not found, create features referenced in the target attribute." />
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158 </section>
2
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159 <expand macro="wait_for"/>
0
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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160 </inputs>
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161 <outputs>
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162 <data format="txt" name="results" label="Load GFF3 into Tripal" />
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163 </outputs>
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164 <tests>
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165 <test expect_failure="true" expect_exit_code="1">
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166 <param name="gff3" value="sample.gff3" />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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167 <param name="organism" value="Testus testus" />
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168 <param name="analysis" value="Annotation xx" />
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169 <conditional name="naming">
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170 <param name="mode" value="manual" />
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171 <param name="re_mrna" value="([a-z]{4}[0-9]+)_rna" />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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172 <param name="re_protein" value="([a-z]{4}[0-9]+)_prot" />
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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173 </conditional>
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174
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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175 <expand macro="test_result" />
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176 </test>
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177 </tests>
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178 <help><![CDATA[
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179 @HELP_OVERVIEW@
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180
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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181 **Load GFF3**
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182
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183 With this tool, you can load features from a GFF3 file into the Tripal/Chado database.
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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185 @HELP@
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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186 ]]></help>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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187 <expand macro="citation"/>
5ce8ae1288c1 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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188 </tool>