tmp add loc file

Author: simonbray

chemicaltoolbox/lirasearch/lirasearch.xml

@@ -10,9 +10,7 @@
         <![CDATA[
             nohup /opt/ignite/bin/ignite.sh config/lira_ignite.xml &
             export HOME=`pwd` &&
-            #if $is_test:
-                cp -r /opt/ignite/test-database/* /opt/ignite/storage &&
-            #end if
+            ln -s ${database_select.fields.path}/* /opt/ignite/storage &&
             #if $ligand.ext == 'pdb':
                 ln -s $ligand ligand.pdb &&
             #else
@@ -28,6 +26,12 @@
     </command>
     <inputs>
         <param name="ligand" type="data" format="pdb,sdf" label="Ligand file" />
+	<param name="database_select" type="select" label="Select database from list">
+	    <options from_data_table="lirasearch">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No databases are available!" />
+	    </options>
+        </param>
         <param name="num_results" type="integer" value="50" label="Number of results to return" />
         <param name="is_test" type="hidden" value="false" />
     </inputs>
@@ -37,13 +41,15 @@
     </outputs>
     <tests>
         <test>
-            <param name="ligand" value="ligand.pdb" ftype="pdb" />
+	    <param name="ligand" value="ligand.pdb" ftype="pdb" />
+	    <param name="database_select" value="test"/>
             <param name="num_results" value="2" />
             <param name="is_test" value="true" />
             <output name="output_sdf" value="lirasearch_output.sdf"/>
         </test>
         <test>
             <param name="ligand" value="ligand.sdf"/>
+	    <param name="database_select" value="test"/>
             <param name="num_results" value="2" />
             <param name="is_test" value="true" />
             <output name="output_sdf" value="lirasearch_output.sdf"/>

chemicaltoolbox/lirasearch/test-data/lirasearch.loc

@@ -0,0 +1,12 @@
+# This file lists databases that can be searched with LiraSearch.
+# The file has the format (white space characters are
+# TAB characters):
+#
+# <unique_id>	<name>	<path>
+#
+# So, lirasearch.loc could look something like this:
+#value  name    path
+#zinc20	ZINC20	/home/galaxy/zinc20
+#zinc22	ZINC22	/home/galaxy/zinc22
+#dude	DUD-E	/home/galaxy/dude
+test	test	${__HERE__}/storage