Fix and expand CWL wrapper (#230 #221)

* add verbose option
* refactor input bindings
* add plasmid parameter
* add locus parameter
* add debug parameter
* refactor JS globs
* fix output of genome sequences

Author: oschwengers

bakta.cwl

@@ -38,35 +38,39 @@ inputs:
     id: db
     inputBinding: {prefix: --db}
     type: Directory
+  - doc: Minimum contig size (default = 1; 200 in compliant mode)
+    id: min_contig_length
+    inputBinding: {prefix: --min-contig-length}
+    type: int?
+  - doc: Prefix for output files
+    id: prefix
+    inputBinding: {prefix: --prefix}
+    type: string?
   - doc: Output directory (default = current working directory)
     id: output
     inputBinding: {prefix: --output}
     type: Directory?
-  - doc: Output files prefix
-    id: prefix
-    inputBinding: {prefix: --prefix}
-    type: string?
-  - doc: Force overwrite output
+  - doc: Force overwriting existing output folder (except for current working directory)
     id: force
     inputBinding: {prefix: --force}
     default: true
     type: boolean?
-  - doc: Min contig length
-    id: min_contig_length
-    inputBinding: {prefix: --min-contig-length}
-    type: int?
-  - doc: Genus
+  - doc: Genus name
     id: genus
     inputBinding: {prefix: --genus}
     type: string?
-  - doc: Species
+  - doc: Species name
     id: species
     inputBinding: {prefix: --species}
     type: string?
-  - doc: Strain
+  - doc: Strain name
     id: strain
     inputBinding: {prefix: --strain}
     type: string?
+  - doc: Plasmid name
+    id: plasmid
+    inputBinding: {prefix: --plasmid}
+    type: string?
   - doc: All sequences are complete replicons (chromosome/plasmid[s])
     id: complete
     inputBinding: {prefix: --complete}
@@ -79,14 +83,18 @@ inputs:
     id: translation_table
     inputBinding: {prefix: --translation-table}
     type: int?
-  - doc: Locus tag
-    id: locus_tag
-    inputBinding: {prefix: --locus-tag}
-    type: string?
   - doc: Gram type (default = ?)
     id: gram
     inputBinding: {prefix: --gram}
     type: string?
+  - doc: Locus prefix (default = contig)
+    id: locus
+    inputBinding: {prefix: --locus}
+    type: string?
+  - doc: Locus tag prefix (default = autogenerated)
+    id: locus_tag
+    inputBinding: {prefix: --locus-tag}
+    type: string?
   - doc: Keep original contig headers
     id: keep_contig_headers
     inputBinding: {prefix: --keep-contig-headers}
@@ -155,14 +163,23 @@ inputs:
     id: skip_plot
     inputBinding: {prefix: --skip-plot}
     type: boolean?
-  - doc: Directory for temporary files (default = system dependent auto detection)
-    id: tmp_dir
-    inputBinding: {prefix: --tmp-dir}
-    type: Directory?
+  - doc: Print verbose information
+    id: verbose
+    inputBinding: {prefix: --verbose}
+    default: true
+    type: boolean?
+  - doc: Run Bakta in debug mode
+    id: debug
+    inputBinding: {prefix: --debug}
+    type: boolean?
   - doc: Threads
     id: threads
     inputBinding: {prefix: --threads}
     type: int?
+  - doc: Directory for temporary files (default = system dependent auto detection)
+    id: tmp_dir
+    inputBinding: {prefix: --tmp-dir}
+    type: Directory?
 
 outputs:
   - doc: Hypothetical CDS AA sequences as Fasta
@@ -182,11 +199,10 @@ outputs:
     outputBinding:
       glob: ${
               if (inputs.prefix !== null) {
-                var out = inputs.prefix+'.tsv';
+                return inputs.prefix + '.tsv';
               } else{
-                var out = inputs.fasta_file.basename.replace(/\.[^/.]+$/, "")+'.tsv';
+                return inputs.fasta_file.basename.replace(/\.[^/.]+$/, '') + '.tsv';
               }
-              return out
             }
   - doc: Annotation summary as txt
     id: summary_txt
@@ -219,7 +235,7 @@ outputs:
     format: edam:format_2200
     outputBinding: {glob: '*.fna'}
   - doc: Gene DNA sequences as Fasta
-    id: sequences_fna
+    id: sequences_ffn
     type: File
     format: edam:format_2200
     outputBinding: {glob: '*.ffn'}
@@ -230,11 +246,10 @@ outputs:
     outputBinding:
       glob: ${
               if (inputs.prefix !== null) {
-                var out = inputs.prefix+'.faa';
+                return inputs.prefix + '.faa';
               } else{
-                var out = inputs.fasta_file.basename.replace(/\.[^/.]+$/, "")+'.faa';
+                return inputs.fasta_file.basename.replace(/\.[^/.]+$/, '') + '.faa';
               }
-              return out
             }
   - doc: Circular genome plot as PNG
     id: plot_png