Add new parameters

Author: pvanheus

galaxy/lukasa.xml

@@ -1,9 +1,9 @@
 <tool id="lukasa" name="Lukasa" version="@TOOL_VERSION@+galaxy0">
     <description>Align protein evidence against genomic contigs using metaeuk and spaln</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.13.0</token>
-        <!-- note that this DOI is for lukasa 0.0.6 - update as needed -->
-        <token name="@DOI@">10.5281/zenodo.7236571</token>
+        <token name="@TOOL_VERSION@">0.14.1</token>
+        <!-- note that this DOI is for lukasa 0.14.0 - update as needed -->
+        <token name="@DOI@">10.5281/zenodo.7339605</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">lukasa</requirement>
@@ -18,6 +18,12 @@
         #end if
         #if str($min_intron).strip():
             --min_intron $min_intron
+        #end if
+        #if str($min_coverage).strip()
+            --min_coverage $min_coverage
+        #end if
+        #if str($eval).strip()
+            --eval $eval
         #end if
             --output_filename '$output_gff' '$contigs_fasta' '$proteins_fasta'
     ]]></command>
@@ -27,8 +33,10 @@
         <param name="species_table" type="text" label="Spaln species table to use (optional)"/>
         <param argument="--max_intron" type="integer" min="0" label="Max intron length" help="Maximum intron length (passed to metaeuk)" optional="true" />
         <param argument="--min_intron" type="integer" min="0" label="Min intron length" help="Minimum intron length (passed to metaeuk and spaln)" optional="true" />
+        <param argument="--min_coverage" type="float" min="0" max="1" label="Min coverage" help="Minimum proportion of a gene that needs to be covered by exons" optional="true" />
+        <param argument="--eval" type="float" min="0" label="E-val" help="Maximum E-val for MetaEuk" optional="true" />
     </inputs>
-    <outputs>
+     <outputs>
         <data name="output_gff" format="gff3" label="Map proteins to genome ${on_string}"/>
     </outputs>
     <tests>

lukasa.py

@@ -16,6 +16,8 @@ def build_template(
     species_table: str = "",
     max_intron: str = "",
     min_intron: str = "",
+    min_coverage: str = "",
+    eval: str = ""
 ):
     template = f"""
     contigs_fasta:
@@ -28,6 +30,8 @@ def build_template(
       path: {protein_path}
     {max_intron}
     {min_intron}
+    {min_coverage}
+    {eval}
     {species_table}
 
     $namespaces:
@@ -59,6 +63,8 @@ def is_fasta(input_filename):
     parser.add_argument("--workflow_dir", default=cwl_workflow_dir)
     parser.add_argument("--max_intron", type=int, help="Maximum intron length")
     parser.add_argument("--min_intron", type=int, help="Minimum intron length")
+    parser.add_argument("--min_coverage", type=float, help="Minimum proportion of a gene that is exons")
+    parser.add_argument("--eval", type=float, help="Maximum E-value for MetaEuk")
     parser.add_argument("--debug", action="store_true", default=False)
     parser.add_argument("contigs_filename", help="File with genomic contigs")
     parser.add_argument("proteins_filename", help="File with proteins to map")
@@ -76,13 +82,19 @@ def is_fasta(input_filename):
         max_intron = f"max_intron: {args.max_intron}\n"
     if args.min_intron is not None:
         min_intron = f"min_intron: {args.min_intron}\n"
+    if args.min_coverage is not None:
+        min_coverage = f'min_coverage: "{args.min_coverage}"\n'
+    if args.eval is not None:
+        eval = f'eval: "{args.eval}"\n'
     cwl_input_file.write(
         build_template(
             abspath(args.contigs_filename),
             abspath(args.proteins_filename),
             species_table=species_table,
             max_intron=max_intron,
             min_intron=min_intron,
+            min_coverage=min_coverage,
+            eval=eval
         )
     )
     cwl_input_file.close()