Mercurial > repos > gga > tripal_db_index
comparison db_index.xml @ 4:0e6e02743484 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 06:19:17 -0500 |
| parents | c1fd973dd914 |
| children | 1d109af32d7c |
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| 3:6fcad55db033 | 4:0e6e02743484 |
|---|---|
| 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" |
| 57 type="text" | 64 type="text" |
| 58 label="Table to index" | 65 label="Table to index" |
| 59 help="The name of a Chado (or custom) table to index" /> | 66 help="The name of a Chado (or custom) table to index" /> |
| 60 <param name="index_name" label="Index Name" argument="--index_name" type="text" help="Index name" /> | 67 <param name="index_name" label="Index Name" argument="--index_name" type="text" help="Index name" /> |
| 61 <repeat name="repeat_fields" title="Fields"> | 68 <repeat name="repeat_fields" title="Fields"> |
| 62 <param name="field_name" | 69 <param name="field_name" |
| 63 label="Field name" | 70 label="Field name" |
| 64 argument="--fields" | 71 argument="--fields" |
| 65 type="text" | 72 type="text" |
| 66 help="Field to index" /> | 73 help="Field to index" /> |
| 67 <param name="field_type" | 74 <param name="field_type" |
| 79 <option value="nested">nested</option> | 86 <option value="nested">nested</option> |
| 80 <option value="geo_point">geo_point</option> | 87 <option value="geo_point">geo_point</option> |
| 81 <option value="geo_shape">geo_shape</option> | 88 <option value="geo_shape">geo_shape</option> |
| 82 <option value="completion">completion</option> | 89 <option value="completion">completion</option> |
| 83 </param> | 90 </param> |
| 84 </repeat> | 91 </repeat> |
| 85 <repeat name="repeat_links" title="Links"> | 92 <repeat name="repeat_links" title="Links"> |
| 86 <param name="column" | 93 <param name="column" |
| 87 label="Table column where to display links" | 94 label="Table column where to display links" |
| 88 type="text" | 95 type="text" |
| 89 help="Should be in the list of indexed column" /> | 96 help="Should be in the list of indexed column" /> |
| 90 <param name="url" | 97 <param name="url" |
| 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** |