md formatting and ordering changes

src/umi_tools/umi_tools_extract/config.vsh.yaml

@@ -16,13 +16,57 @@ references:
 license: MIT
 
 argument_groups:
-  - name: Extract Options
+
+  - name: Input
+    arguments: 
+    - name: --paired
+      type: boolean_true
+      description: Paired fastq files. If option is set, two input files are expected.
+    - name: --input
+      type: file
+      required: true
+      description: Input fastq files, either one or two (paired).
+      example: sample.fastq
+    - name: --read2_in
+      type: file
+      description: Filename for read pairs.
+    - name: --bc_pattern
+      type: string
+      description: |
+        The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides 
+        of the read are from the UMI.
+    - name: --bc_pattern2
+      type: string
+      description: The UMI barcode pattern to use for read 2.
+
+  - name: "Output"
+    arguments:  
+    - name: --read1_out
+      type: file
+      required: true
+      description: Output file for read 1.
+      direction: output
+    - name: --read2_out
+      type: file
+      description: Output file for read 2.
+      direction: output
+    - name: --filtered_out
+      type: file
+      description: |
+        Write out reads not matching regex pattern or cell barcode whitelist to this file.
+    - name: --filtered_out2
+      type: file
+      description: |
+        Write out read pairs not matching regex pattern or cell barcode whitelist to this file.
+
+    - name: Extract Options
     arguments:
     - name: --umitools_extract_method
       alternatives: --extract_method
       type: string
       choices: [string, regex]
-      description: UMI pattern to use. [string]
+      description: |
+        UMI pattern to use. Default: `string`.
       example: "string"
     - name: --error_correct_cell
       type: boolean_true
@@ -36,18 +80,17 @@ argument_groups:
         column will be ignored.
     - name: --blacklist
       type: file
-      description: BlackWhitelist of cell barcodes to discard
+      description: BlackWhitelist of cell barcodes to discard.
     - name: --subset_reads
       type: integer
-      description: Only parse the first N reads
+      description: Only parse the first N reads.
     - name: --quality_filter_threshold
       type: integer
-      description: |
-        Remove reads where any UMI base quality score falls below this threshold
+      description: Remove reads where any UMI base quality score falls below this threshold.
     - name: --quality_filter_mask
       type: string
       description: |
-        If a UMI base has a quality below this threshold, replace the base with 'N'
+        If a UMI base has a quality below this threshold, replace the base with 'N'.
     - name: --quality_encoding
       type: string
       choices: [phred33, phred64, solexa]
@@ -68,77 +111,12 @@ argument_groups:
       description: |
         By default the barcode is assumed to be on the 5' end of the read, but use this option to sepecify that it is
         on the 3' end instead. This option only works with --extract_method=string since 3' encoding can be specified
-        explicitly with a regex, e.g .*(?P<umi_1>.{5})$
+        explicitly with a regex, e.g `.*(?P<umi_1>.{5})$`.
     - name: --ignore_read_pair_suffixes
       type: boolean_true
       description: |
         Ignore "/1" and "/2" read name suffixes. Note that this options is required if the suffixes are not whitespace
-        separated from the rest of the read name
-
-  - name: Input
-    arguments: 
-    - name: --paired
-      type: boolean_true
-      description: Paired fastq files. If option is set, two input files are expected.
-    - name: --input
-      type: file
-      required: true
-      description: Input fastq files, either one or two (paired).
-      example: sample.fastq
-    - name: --read2_in
-      type: file
-      description: Filename for read pairs
-    - name: --bc_pattern
-      type: string
-      description: |
-        The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides 
-        of the read are from the UMI.
-    - name: --bc_pattern2
-      type: string
-      description: The UMI barcode pattern to use for read 2.
-
-  - name: "Output"
-    arguments:  
-    - name: --read1_out
-      type: file
-      required: true
-      description: Output file for read 1.
-      direction: output
-    - name: --read2_out
-      type: file
-      description: Output file for read 2.
-      direction: output
-    - name: --filtered_out
-      type: file
-      description: |
-        Write out reads not matching regex pattern or cell barcode whitelist to this file
-    - name: --filtered_out2
-      type: file
-      description: |
-        Write out read pairs not matching regex pattern or cell barcode whitelist to this file
-
-
-  - name: Additional arguments
-    arguments:
-    - name: --umitools_umi_separator
-      alternatives: --umi_separator
-      type: string
-      default: "_"
-      description: |
-        The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with
-        UMI-tools and used other software.
-    - name: --umitools_grouping_method
-      type: string
-      choices: [unique, percentile, cluster, adjacency, directional]
-      description: |
-        Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying
-        the reads with the same mapping position, but treat similar yet nonidentical UMIs differently. [directional]
-      example: "directional"
-    - name: --umi_discard_read
-      type: integer
-      choices: [0, 1, 2]
-      description: After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. [0]
-      example: 0
+        separated from the rest of the read name.
 
   - name: Common Options
     arguments:
@@ -164,7 +142,8 @@ argument_groups:
     - name: --compresslevel
       type: integer
       description: |
-        Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9). [6]
+        Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9).
+        Default `6`.
       example: 6
     - name: --timeit
       type: file