comparison db_index.xml @ 5:c1df80f03ba6 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author gga
date Mon, 25 Feb 2019 05:50:30 -0500
parents 19d21d9c6656
children 37e46b23109f
comparison
equal deleted inserted replaced
4:19d21d9c6656 5:c1df80f03ba6
36 #for $rep in $table.repeat_links: 36 #for $rep in $table.repeat_links:
37 --links "${rep.column}|${rep.url}" 37 --links "${rep.column}|${rep.url}"
38 #end for 38 #end for
39 #end if 39 #end if
40 40
41 #if $expose.do_expose == "yes":
42 --exposed
43 --index_url '${expose.index_url}'
44 #end if
45
41 && 46 &&
42 47
43 echo "Data loaded" > $results 48 echo "Data loaded" > $results
44 ]]></command> 49 ]]></command>
45 <inputs> 50 <inputs>
47 <param name="mode" 52 <param name="mode"
48 type="select" 53 type="select"
49 label="Data to index"> 54 label="Data to index">
50 <option value="website" selected="true">Index all the Tripal content</option> 55 <option value="website" selected="true">Index all the Tripal content</option>
51 <option value="table">Index a specific table</option> 56 <option value="table">Index a specific table</option>
57 <option value="nodes">Index all website nodes</option>
58 <option value="entities">Index all website entities (Tripal 3 only)</option>
52 </param> 59 </param>
53 <when value="website"/> 60 <when value="website"/>
54 <when value="table"> 61 <when value="table">
55 <param name="table" 62 <param name="table"
56 argument="--table" 63 argument="--table"
91 label="Links url" 98 label="Links url"
92 type="text" 99 type="text"
93 help="e.g.: /your/url/[any-column-name]"/> 100 help="e.g.: /your/url/[any-column-name]"/>
94 </repeat> 101 </repeat>
95 </when> 102 </when>
103 <when value="nodes"/>
104 <when value="entities"/>
96 </conditional> 105 </conditional>
97 <param name="tokenizer" 106 <param name="tokenizer"
98 type="select" 107 type="select"
99 label="Tokenizer to use"> 108 label="Tokenizer to use">
100 <option value="standard" selected="true">standard</option> 109 <option value="standard" selected="true">standard</option>
108 <option value="keyword">keyword</option> 117 <option value="keyword">keyword</option>
109 <option value="pattern">pattern</option> 118 <option value="pattern">pattern</option>
110 <option value="path_hierarchy">path_hierarchy</option> 119 <option value="path_hierarchy">path_hierarchy</option>
111 </param> 120 </param>
112 <param name="queues" label="Queues" argument="queues" type="integer" value="10" help="Number of indexing task queues" /> 121 <param name="queues" label="Queues" argument="queues" type="integer" value="10" help="Number of indexing task queues" />
122 <conditional name="expose">
123 <param name="do_expose" type="select" label="Expose the index to other websites (read-only)">
124 <option value="yes" selected="true">Yes</option>
125 <option value="no">No</option>
126 </param>
127 <when value="no"/>
128 <when value="yes">
129 <param name="index_url" label="Index Url" argument="--index_url" type="text" help="In order for other sites to link back to your results page, you must specify a path where the form for this index can be reached" />
130 </when>
131 <when value="nodes"/>
132 <when value="entities"/>
133 </conditional>
113 <expand macro="wait_for"/> 134 <expand macro="wait_for"/>
114 </inputs> 135 </inputs>
115 <outputs> 136 <outputs>
116 <data format="txt" name="results" label="Index Tripal data" /> 137 <data format="txt" name="results" label="Index Tripal data" />
117 </outputs> 138 </outputs>
130 <param name="fields" value="genus species description" /> 151 <param name="fields" value="genus species description" />
131 </conditional> 152 </conditional>
132 153
133 <expand macro="test_result" /> 154 <expand macro="test_result" />
134 </test> 155 </test>
156 <test expect_failure="true" expect_exit_code="1">
157 <conditional name="table">
158 <param name="mode" value="singles" />
159 <param name="table" value="organism" />
160 <param name="fields" value="genus species description" />
161 </conditional>
162 <conditional name="expose">
163 <param name="expose" value="yes" />
164 <param name="index_url" value="http://google.com" />
165 </conditional>
166
167 <expand macro="test_result" />
168 </test>
135 </tests> 169 </tests>
136 <help><![CDATA[ 170 <help><![CDATA[
137 @HELP_OVERVIEW@ 171 @HELP_OVERVIEW@
138 172
139 **Index using Elasticsearch** 173 **Index using Elasticsearch**