Add choices fields and change default fields to exampels

src/umi_tools/umi_tools_dedup/config.vsh.yaml

@@ -58,10 +58,14 @@ argument_groups:
           in the file names.
       - name: --extract_umi_method
         type: string
+        choices: ["read_id", "tag", "umis"]
         description: |
           Specify the method by which the barcodes were encoded in the read.
-          The options are: [read_id, tag, umis].
-        default: read_id
+          The options are:
+            * read_id (default) 
+            * tag
+            * umis
+        example: "read_id"
       - name: --umi_tag
         type: string
         description: |
@@ -71,8 +75,8 @@ argument_groups:
         type: string
         description: |
           The separator used to separate the UMI from the read sequence. 
-          This is only required if the extract_umi_method is set to id_read.
-        default: '_'
+          This is only required if the extract_umi_method is set to id_read. ['_']
+        example: '_'
       - name: --umi_tag_split
         type: string
         description: |
@@ -99,17 +103,23 @@ argument_groups:
     arguments:    
       - name: --method
         type: string
-        description: |
-          The method to use for grouping reads. The options are: 
-          [unique, percentile, cluster, adjacency, directional].
-        default: directional
+        choices: ["unique", "percentile", "cluster", "adjacency", "directional"]
+        description: |
+          The method to use for grouping reads. 
+          The options are: 
+            * unique
+            * percentile
+            * cluster
+            * adjacency
+            * directional (default)
+        example: "directional"
       - name: --edit_distance_threshold
         type: integer
         description: |
           For the adjacency and cluster methods the threshold for the edit 
           distance to connect two UMIs in the network can be increased. The 
-          default value of 1 works best unless the UMI is very long (>14bp).
-        default: 1
+          default value of 1 works best unless the UMI is very long (>14bp). [1]
+        example: 1
       - name: --spliced_is_unique
         type: boolean_true
         description: |
@@ -122,8 +132,8 @@ argument_groups:
           Mappers that soft clip will sometimes do so rather than mapping a
           spliced read if there is only a small overhang over the exon junction.
           By setting this option, you can treat reads with at least this many
-          bases soft-clipped at the 3' end as spliced.
-        default: 4
+          bases soft-clipped at the 3' end as spliced. [4]
+        example: 4
       - name: --multimapping_detection_method
         type: string
         description: |
@@ -188,39 +198,37 @@ argument_groups:
       - name: --mapping_quality
         type: integer
         description: |
-          Minimium mapping quality (MAPQ) for a read to be retained.
-        default: 0
+          Minimium mapping quality (MAPQ) for a read to be retained. [0]
+        example: 0
       - name: --unmapped_reads
         type: string
         description: |
           How unmapped reads should be handled. 
           The options are:
-          "discard": Discard all unmapped reads.
-          "use":     If read2 is unmapped, deduplicate using read1 only. 
-                     Requires --paired.
-          "output":  Output unmapped reads/read pairs without UMI 
-                     grouping/deduplication. Only available in umi_tools group.
-        default: discard
+            * "discard": Discard all unmapped reads. (default)
+            * "use":     If read2 is unmapped, deduplicate using read1 only. Requires --paired.
+            * "output":  Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.
+        example: "discard"
       - name: --chimeric_pairs
         type: string
+        choices: ["discard", "use", "output"]
         description: |
           How chimeric pairs should be handled. 
           The options are:
-          "discard": Discard all chimeric read pairs.
-          "use":     Deduplicate using read1 only.
-          "output":  Output chimeric pairs without UMI grouping/deduplication. 
-                     Only available in umi_tools group.
-        default: use
+            * "discard": Discard all chimeric read pairs.
+            * "use":     Deduplicate using read1 only. (default)
+            * "output":  Output chimeric pairs without UMI grouping/deduplication. Only available in umi_tools group.
+        example: "use"
       - name: --unpaired_reads
         type: string
+        choices: ["discard", "use", "output"]
         description: |
           How unpaired reads should be handled. 
-          The options are:
-          "discard": Discard all unpaired reads.
-          "use":     Deduplicate using read1 only.
-          "output":  Output unpaired reads without UMI grouping/deduplication. 
-                     Only available in umi_tools group.
-        default: use
+          The options are: 
+            * "discard": Discard all unmapped reads.
+            * "use": If read2 is unmapped, deduplicate using read1 only. Requires --paired. (default)
+            * "output":  Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.
+        example: "use"
       - name: --ignore_umi
         type: boolean_true
         description: |
@@ -266,8 +274,8 @@ argument_groups:
       - name: --verbose
         alternatives: -v
         type: integer
-        description: Log level. The higher, the more output.
-        default: 0
+        description: Log level. The higher, the more output. [0]
+        example: 0
       - name: --error
         alternatives: -E
         type: file
@@ -279,15 +287,15 @@ argument_groups:
       - name: --compresslevel
         type: integer
         description: |
-          Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default.
-        default: 6
+          Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default. [6]
+        example: 6
       - name: --timeit
         type: file
         description: Store timing information in file.
       - name: --timeit_name
         type: string
-        description: Name in timing file for this class of jobs.
-        default: "all"
+        description: Name in timing file for this class of jobs. [all]
+        example: "all"
       - name: --timeit_header
         type: string
         description: Add header for timing information.