diff db_index.xml @ 4:0e6e02743484 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39

--- a/db_index.xml	Mon Aug 06 04:44:27 2018 -0400
+++ b/db_index.xml	Mon Feb 25 06:19:17 2019 -0500
@@ -38,6 +38,11 @@
                 #end for
             #end if
 
+            #if $expose.do_expose == "yes":
+                --exposed
+                --index_url '${expose.index_url}'
+            #end if
+
         &&
 
         echo "Data loaded" > $results
@@ -49,6 +54,8 @@
                    label="Data to index">
                 <option value="website" selected="true">Index all the Tripal content</option>
                 <option value="table">Index a specific table</option>
+                <option value="nodes">Index all website nodes</option>
+                <option value="entities">Index all website entities (Tripal 3 only)</option>
             </param>
             <when value="website"/>
             <when value="table">
@@ -59,7 +66,7 @@
                        help="The name of a Chado (or custom) table to index" />
                 <param name="index_name" label="Index Name" argument="--index_name" type="text" help="Index name" />
                 <repeat name="repeat_fields" title="Fields">
-            		<param name="field_name"
+                    <param name="field_name"
                            label="Field name"
                            argument="--fields"
                            type="text"
@@ -81,9 +88,9 @@
                         <option value="geo_shape">geo_shape</option>
                         <option value="completion">completion</option>
                     </param>
-            	</repeat>
-            	<repeat name="repeat_links" title="Links">
-            		<param name="column"
+                </repeat>
+                <repeat name="repeat_links" title="Links">
+                    <param name="column"
                            label="Table column where to display links"
                            type="text"
                            help="Should be in the list of indexed column" />
@@ -91,8 +98,10 @@
                            label="Links url"
                            type="text"
                            help="e.g.: /your/url/[any-column-name]"/>
-            	</repeat>
+                </repeat>
             </when>
+            <when value="nodes"/>
+            <when value="entities"/>
         </conditional>
         <param name="tokenizer"
                type="select"
@@ -110,6 +119,18 @@
             <option value="path_hierarchy">path_hierarchy</option>
         </param>
         <param name="queues" label="Queues" argument="queues" type="integer" value="10" help="Number of indexing task queues" />
+        <conditional name="expose">
+            <param name="do_expose" type="select" label="Expose the index to other websites (read-only)">
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <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" />
+            </when>
+            <when value="nodes"/>
+            <when value="entities"/>
+        </conditional>
         <expand macro="wait_for"/>
     </inputs>
     <outputs>
@@ -132,6 +153,19 @@
 
             <expand macro="test_result" />
         </test>
+        <test expect_failure="true" expect_exit_code="1">
+            <conditional name="table">
+                <param name="mode" value="singles" />
+                <param name="table" value="organism" />
+                <param name="fields" value="genus species description" />
+            </conditional>
+            <conditional name="expose">
+                <param name="expose" value="yes" />
+                <param name="index_url" value="http://google.com" />
+            </conditional>
+
+            <expand macro="test_result" />
+        </test>
     </tests>
     <help><![CDATA[
         @HELP_OVERVIEW@