changeset 10:072c324f20fc draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573

--- a/alphafold.xml	Tue Sep 13 22:04:12 2022 +0000
+++ b/alphafold.xml	Fri Sep 16 02:19:37 2022 +0000
@@ -2,7 +2,7 @@
     <description> - AI-guided 3D structural prediction of proteins</description>
     <macros>
       <token name="@TOOL_VERSION@">2.1.2</token>
-      <token name="@VERSION_SUFFIX@">2</token>
+      <token name="@VERSION_SUFFIX@">3</token>
     </macros>
     <edam_topics>
       <edam_topic>topic_0082</edam_topic>
@@ -47,13 +47,20 @@
 --fasta_paths alphafold.fasta
 --output_dir output
 --data_dir \${ALPHAFOLD_DB:-/data}
---uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
---mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa
---template_mmcif_dir   \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
---obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
 --max_template_date=\$DATE
---bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
+
+## Set reference data explicitly
+--uniref90_database_path   \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
+--mgnify_database_path     \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa
+--template_mmcif_dir       \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
+--obsolete_pdbs_path       \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
+#if $dbs == 'full':
+--bfd_database_path        \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08
+#else
+--db_preset=reduced_dbs
+--small_bfd_database_path  \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta
+#end if
 
 ## Param introduced in AlphaFold v2.1.2:
 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
@@ -102,6 +109,18 @@
         </conditional>
 
         <param
+          name="dbs"
+          type="select"
+          display="radio"
+          label="Select database"
+          help="The reduced database allows significantly faster run time in
+            exchange for a small loss in accuracy."
+        >
+          <option value="reduced" selected="true">Reduced database</option>
+          <option value="full">Full database</option>
+        </param>
+
+        <param
           name="multimer"
           type="boolean"
           checked="false"