From 0bcb8742ed6f14d40f41ca540072fe25d6e4bbcd Mon Sep 17 00:00:00 2001
From: Peter van Heusden <pvh@sanbi.ac.za>
Date: Tue, 13 Oct 2020 11:37:45 +0200
Subject: [PATCH] Make species_table param optional

---
 conda/meta.yaml              |  2 +-
 lukasa.py                    | 10 +++++++---
 protein_evidence_mapping.cwl |  2 +-
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/conda/meta.yaml b/conda/meta.yaml
index f653204..6adec57 100644
--- a/conda/meta.yaml
+++ b/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.
diff --git a/lukasa.py b/lukasa.py
index 581d15e..a3abd53 100644
--- a/lukasa.py
+++ b/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()
diff --git a/protein_evidence_mapping.cwl b/protein_evidence_mapping.cwl
index 8693ddf..7966d5e 100644
--- a/protein_evidence_mapping.cwl
+++ b/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