Mercurial > repos > gga > tripal_db_index

annotate db_index.xml @ 0:e7f577d73cf6 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:42:22 -0400
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children 9526ebfdafe2
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e7f577d73cf6 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?>
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2 <tool id="db_index" profile="16.04" name="Index Tripal data" version="@WRAPPER_VERSION@.0">
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3 <description>using Elasticsearch</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 <expand macro="stdio"/>
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9 <command><![CDATA[
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10
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11 @AUTH@
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12
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13 tripaille db index
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14
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15 --mode '${table.mode}'
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16
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17 #if $table.mode == "table":
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18 --index_name "${table.index_name}"
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19 #end if
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20
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21 #if $queues:
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22 --queues "$queues"
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23 #end if
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25 #if $tokenizer:
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26 --tokenizer "$tokenizer"
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27 #end if
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28
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29 #if $table.mode == "table":
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30 --table '${table.table}'
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31
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32 #for $rep in $table.repeat_fields:
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33 --fields "${rep.field_name}|${rep.field_type}"
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34 #end for
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35
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36 #for $rep in $table.repeat_links:
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37 --links "${rep.column}|${rep.url}"
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38 #end for
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39 #end if
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40
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41 &&
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42
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43 echo "Data loaded" > $results
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44 ]]></command>
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45 <inputs>
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46 <conditional name="table">
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47 <param name="mode"
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48 type="select"
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49 label="Data to index">
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50 <option value="website" selected="true">Index all the Tripal content</option>
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51 <option value="table">Index a specific table</option>
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52 </param>
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53 <when value="website"/>
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54 <when value="table">
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55 <param name="table"
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56 argument="--table"
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57 type="text"
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58 label="Table to index"
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59 help="The name of a Chado (or custom) table to index" />
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60 <param name="index_name" label="Index Name" argument="--index_name" type="text" help="Index name" />
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61 <repeat name="repeat_fields" title="Fields">
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62 <param name="field_name"
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63 label="Field name"
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64 argument="--fields"
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65 type="text"
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66 help="Field to index" />
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67 <param name="field_type"
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68 label="Field
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69 type" type="select"
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70 help="Field type">
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71 <option value="string" selected="true">string</option>
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72 <option value="keyword">keyword</option>
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73 <option value="date">date</option>
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74 <option value="long">long</option>
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75 <option value="double">double</option>
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76 <option value="boolean">boolean</option>
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77 <option value="ip">ip</option>
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78 <option value="object">object</option>
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79 <option value="nested">nested</option>
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80 <option value="geo_point">geo_point</option>
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81 <option value="geo_shape">geo_shape</option>
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82 <option value="completion">completion</option>
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83 </param>
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84 </repeat>
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85 <repeat name="repeat_links" title="Links">
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86 <param name="column"
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87 label="Table column where to display links"
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88 type="text"
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89 help="Should be in the list of indexed column" />
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90 <param name="url"
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91 label="Links url"
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92 type="text"
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93 help="e.g.: /your/url/[any-column-name]"/>
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94 </repeat>
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95 </when>
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96 </conditional>
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97 <param name="tokenizer"
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98 type="select"
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99 label="Tokenizer to use">
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100 <option value="standard" selected="true">standard</option>
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101 <option value="letter">letter</option>
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102 <option value="lowercase">lowercase</option>
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103 <option value="whitespace">whitespace</option>
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104 <option value="uax_url_email">uax_url_email</option>
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105 <option value="classic">classic</option>
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106 <option value="ngram">ngram</option>
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107 <option value="edge_ngram">edge_ngram</option>
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108 <option value="keyword">keyword</option>
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109 <option value="pattern">pattern</option>
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110 <option value="path_hierarchy">path_hierarchy</option>
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111 </param>
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112 <param name="queues" label="Queues" argument="queues" type="integer" value="10" help="Number of indexing task queues" />
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113 </inputs>
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114 <outputs>
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115 <data format="txt" name="results" label="Index Tripal data" />
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116 </outputs>
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117 <tests>
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118 <test expect_failure="true" expect_exit_code="1">
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119 <conditional name="table">
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120 <param name="mode" value="all" />
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121 </conditional>
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122
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123 <expand macro="test_result" />
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124 </test>
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125 <test expect_failure="true" expect_exit_code="1">
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126 <conditional name="table">
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127 <param name="mode" value="singles" />
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128 <param name="table" value="organism" />
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129 <param name="fields" value="genus species description" />
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130 </conditional>
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131
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132 <expand macro="test_result" />
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 @HELP_OVERVIEW@
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137
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138 **Index using Elasticsearch**
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139
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140 With this tool, you can trigger indexing of a Tripal instance content using Elasticsearch.
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141
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142 The `tripal_elasticsearch <http://github.com/tripal/tripal_elasticsearch>`_ module must be installed and configured on the Tripal instance.
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143
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144 @HELP@
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145 ]]></help>
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146 <expand macro="citation"/>
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147 </tool>