changeset 6:34171fd6daed draft

planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit ecc87b04e2f486f941c6eb4746738690db3a9e94-dirty

--- a/data_manager/mob_suite_build_database.py	Fri May 24 15:42:22 2019 -0400
+++ b/data_manager/mob_suite_build_database.py	Fri Jun 21 20:08:15 2019 -0400
@@ -10,27 +10,30 @@
 import string
 import subprocess
 import sys
+import uuid
 
 
 DATA_TABLE_NAME = "mob_suite_databases"
 
 
-def mob_suite_build_database_mob_init(target_directory, data_table_name=DATA_TABLE_NAME):
+def mob_suite_build_database_mob_cluster(target_directory, mob_cluster_args, database_name, data_table_name=DATA_TABLE_NAME):
 
     now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
 
-    database_value = "_".join([
-    ])
+    database_value = uuid.uuid4()
 
-    database_name = " ".join([
-    ])
+    database_name = database_name
 
-    database_path = database_value
+    database_path = mob_cluster_args['outdir']
 
     args = [
+        '--num_threads', mob_cluster_args['num_threads'],
+        '--infile', mob_cluster_args['infile'],
+        '--outdir', mob_cluster_args['outdir'],
+        '--mode', mob_cluster_args['mode'],
     ]
 
-    subprocess.check_call(['mob_init'], cwd=target_directory)
+    subprocess.check_call(['mob_cluster'] + args, cwd=target_directory)
 
     data_table_entry = {
         "data_tables": {
@@ -50,8 +53,9 @@
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('data_manager_json')
-    parser.add_argument( '--threads', dest='threads', default=1, help='threads' )
-    parser.add_argument( '--mode', dest='mode', default=1, help='database construction mode' )
+    parser.add_argument('--threads', dest='threads', default=1, help='threads')
+    parser.add_argument('--input', dest='input', help='Plasmid Assemblies (.fasta)')
+    parser.add_argument('--database-name', dest='database_name', help='Database Name')
     args = parser.parse_args()
 
     data_manager_input = json.loads(open(args.data_manager_json).read())
@@ -68,12 +72,18 @@
 
     data_manager_output = {}
 
-    if str(args.mode) == 'mob_init':
-        data_manager_output = mob_suite_build_database_mob_init(
-            target_directory,
-        )
-    else:
-        sys.exit("Invalid database construction mode")
+    mob_cluster_args = {
+        'num_threads': args.threads,
+        'infile': args.input,
+        'mode': 'build'
+    }
+    
+    data_manager_output = mob_suite_build_database_mob_cluster(
+        target_directory,
+        mob_cluster_args,
+        args.database_name,
+    )
+
 
     open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
 

--- a/data_manager/mob_suite_build_database.xml	Fri May 24 15:42:22 2019 -0400
+++ b/data_manager/mob_suite_build_database.xml	Fri Jun 21 20:08:15 2019 -0400
@@ -10,17 +10,11 @@
         python '$__tool_directory__/mob_suite_build_database.py'
           '${out_file}'
           --threads \${GALAXY_SLOTS:-1}
-          --mode ${mode.mode}
+          --input '${input}'
     ]]>
     </command>
     <inputs>
-        <conditional name="mode">
-            <param name="mode" type="select" multiple="false" label="Mode">
-                <option value="mob_init">Initialize Standard Database (mob_init)</option>
-            </param>
-            <when value="mob_init">
-            </when>
-        </conditional>
+        <param name="input" type="data" multiple="true" label="Plasmid Assemblies" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />