Add extra arguments

src/bgzip/config.vsh.yaml

@@ -9,28 +9,85 @@ functionality:
   requirements:
     cpus: 1
     commands: [ bgzip ]
-  arguments:
-    - name: --input
-      type: file
-      direction: input
-      description: file to be compressed or decompressed
-      required: true
-    - name: --output
-      type: file
-      direction: output
-      description: compressed or decompressed output
-      required: true
-    - name: --decompress
-      alternatives: -d
-      type: boolean_true
-      description: decompress the input file
+  argument_groups:
+    - name: Inputs
+      arguments:
+      - name: --input
+        type: file
+        direction: input
+        description: file to be compressed or decompressed
+        required: true
+    - name: Outputs
+      arguments:
+      - name: --output
+        type: file
+        direction: output
+        description: compressed or decompressed output
+        required: true
+      - name: --index_name
+        alternatives: -I
+        type: file
+        direction: output
+        description: name of BGZF index file [file.gz.gzi]
+    - name: Arguments
+      arguments:
+      - name: offset
+        alternatives: -b
+        type: integer
+        description: decompress at virtual file pointer (0-based uncompressed offset)
+      - name: --decompress
+        alternatives: -d
+        type: boolean_true
+        description: decompress the input file
+      - name: --rebgzip
+        alternatives: -g
+        type: boolean_true
+        description: use an index file to bgzip a file
+      - name: --index
+        alternatives: -i
+        type: boolean_true
+        description: compress and create BGZF index
+      - name: --compress_level
+        alternatives: -l
+        type: integer
+        description: compression level to use when compressing; 0 to 9, or -1 for default [-1]
+        min: -1
+        max: 9
+      - name: --reindex
+        alternatives: -r
+        type: boolean_true
+        description: (re)index the output file
+      - name: --size
+        alternatives: -s
+        type: integer
+        description: decompress INT bytes (uncompressed size)
+        min: 0
+      - name: --test
+        alternatives: -t
+        type: boolean_true
+        description: test integrity of compressed file
+      - name: --binary
+        type: boolean_true
+        description: Don't align blocks with text lines
   resources:
     - type: bash_script
       text: |
         [[ "$par_decompress" == "false" ]] && unset par_decompress
+        [[ "$par_rebgzip" == "false" ]] && unset par_rebgzip
+        [[ "$par_index" == "false" ]] && unset par_index
+        [[ "$par_reindex" == "false" ]] && unset par_reindex
+        [[ "$par_test" == "false" ]] && unset par_test
+        [[ "$par_binary" == "false" ]] && unset par_binary
         bgzip -c \
           ${meta_cpus:+--threads "${meta_cpus}"} \
           ${par_decompress:+-d} \
+          ${par_rebgzip:+-g} \
+          ${par_index:+-i} \
+          ${par_index_name:+-I "${par_index_name}"} \
+          ${par_compress_level:+-l "${par_compress_level}"} \
+          ${par_reindex:+-r} \
+          ${par_size:+-s "${par_size}"} \
+          ${par_test:+-t} \
           "$par_input" > "$par_output"
   test_resources:
     - type: bash_script

src/bgzip/help.txt

@@ -1,3 +1,6 @@
+```bash
+bgzip -h
+```
 
 Version: 1.19
 Usage:   bgzip [OPTIONS] [FILE] ...