Make species_table param optional

conda/meta.yaml

@@ -36,5 +36,5 @@ about:
   summary: "Fast and accurate mapping of proteins against eukaryotic genomes"
   description: |
     Lukasa combines MetaEUK and spaln to rapidly identify matches between proteins and genomic contigs and
-    accurately map the proteins to the identified regions. The output is GFF3, suitable for use in 
+    accurately align the proteins to the identified regions. The output is GFF3 format, suitable for use in 
     eukaryotic genome annotation.

lukasa.py

@@ -16,7 +16,7 @@
   class: File
   format: edam:format_1929
   path: {}
-species_table: {}
+{}
 
 $namespaces:
   edam: http://edamontology.org/
@@ -46,15 +46,19 @@ def is_fasta(input_filename):
     parser.add_argument("--workflow_dir", default=cwl_workflow_dir)
     parser.add_argument("contigs_filename", help="File with genomic contigs")
     parser.add_argument("proteins_filename", help="File with proteins to map")
-    parser.add_argument("species_table", help="spaln species table to use")
+    parser.add_argument("--species_table", help="spaln species table to use")
     args = parser.parse_args()
     if not is_fasta(args.contigs_filename) or not is_fasta(args.proteins_filename):
         sys.exit("Error: Input files must be in FASTA format")
 
     cwl_input_file = tempfile.NamedTemporaryFile(delete=False, mode="w")
+    if args.species_table is not None:
+        species_table_string = 'species_table: {}'.format(args.species_table)
+    else:
+        species_table_string = ''
     cwl_input_file.write(
         template.format(
-            abspath(args.contigs_filename), abspath(args.proteins_filename), args.species_table
+            abspath(args.contigs_filename), abspath(args.proteins_filename), species_table_string
         )
     )
     cwl_input_file.close()

protein_evidence_mapping.cwl

@@ -10,7 +10,7 @@ inputs:
     type: File
     format: edam:format_1929
   species_table:
-    type: string
+    type: string?
 outputs:
   spaln_out:
     type: File