From 474109eb7976741024fb3e4391c7eee769ee9509 Mon Sep 17 00:00:00 2001 From: emmarousseau Date: Mon, 1 Jul 2024 17:31:37 +0100 Subject: [PATCH] Add choices fields and change default fields to exampels --- src/umi_tools/umi_tools_dedup/config.vsh.yaml | 82 ++++++++++--------- 1 file changed, 45 insertions(+), 37 deletions(-) diff --git a/src/umi_tools/umi_tools_dedup/config.vsh.yaml b/src/umi_tools/umi_tools_dedup/config.vsh.yaml index 7c54369a..5b03a6e5 100644 --- a/src/umi_tools/umi_tools_dedup/config.vsh.yaml +++ b/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.