tidy up wrapper

Author: simonbray

chemicaltoolbox/lirasearch/lirasearch.xml

@@ -8,7 +8,6 @@
     </requirements>
     <command detect_errors="exit_code">
         <![CDATA[
-	    ln -sf ${database_select.fields.path}/* /opt/storage/ &&
             export HOME=`pwd` &&
             #if $ligand.ext == 'pdb':
                 ln -s $ligand ligand.pdb &&
@@ -19,14 +18,14 @@
             esp-surface-generator ligand.pdb.pqr ligand.pdb.tmesh &&
             sh-coeff-calculator . &&
             micromamba run -n lirasearch python /opt/scripts/lira_search_sdf.py --in_file rid_coeffs.csv --out_file output --out_keys keys.txt --database /opt/storage/rid_coeffs.csv --num_results $num_results &&
-	    mkdir search_results && rocksdb_to_sdf /opt/storage keys.txt search_results &&
+	    mkdir search_results && rocksdb_to_sdf ${database_select.fields.path} keys.txt search_results &&
 	    micromamba run -n lirasearch python /opt/scripts/lira_super.py --target ligand.pdb --folder search_results &&
             cat search_results/*rotated.sdf >> '$output_sdf'
             ]]>
     </command>
     <inputs>
-        <param name="ligand" type="data" format="pdb,sdf" label="Ligand file" />
-	<param name="database_select" type="select" label="Select database from list">
+        <param name="ligand" type="data" format="pdb,sdf" label="Ligand file" help="Query for searching database" />
+        <param name="database_select" type="select" label="Select database to search">
 	    <options from_data_table="lirasearch">
                 <filter type="sort_by" column="2" />
                 <validator type="no_options" message="No databases are available!" />
@@ -35,7 +34,6 @@
         <param name="num_results" type="integer" value="50" label="Number of results to return" />
     </inputs>
     <outputs>
-        <!-- <data name="output_csv" format="csv" label="Similarity scores" /> -->
         <data name="output_sdf" format="sdf" label="SDF with LiraSearch query results" />
     </outputs>
     <tests>
@@ -63,6 +61,7 @@ Identify similar conformers to an input ligand, based on predicting the electros
 ]]>
     </help>
     <citations>
+        <citation type="doi">10.1101/2022.01.19.476747</citation>
         <citation type="doi">10.1021/acs.jmedchem.9b01129</citation>
     </citations>
 </tool>