mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-24 11:48:17 +00:00
106 lines
2.6 KiB
YAML
106 lines
2.6 KiB
YAML
|
name: "hmmer_eslalimask"
|
||
|
|
description: Mask multiple sequence alignments
|
||
|
|
keywords:
|
||
|
|
- hmmer
|
||
|
|
- alignment
|
||
|
|
- mask
|
||
|
|
tools:
|
||
|
|
- "hmmer":
|
||
|
|
description: "Biosequence analysis using profile hidden Markov models"
|
||
|
|
homepage: http://hmmer.org/
|
||
|
|
documentation: http://hmmer.org/documentation.html
|
||
|
|
tool_dev_url: None
|
||
|
|
doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
|
||
|
|
licence: ["BSD-3-Clause"]
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test' ]
|
||
|
|
|
||
|
|
- unmaskedaln:
|
||
|
|
type: file
|
||
|
|
description: multiple sequence alignment, Stockholm or other formats
|
||
|
|
pattern: "*"
|
||
|
|
|
||
|
|
- fmask_rf:
|
||
|
|
type: val
|
||
|
|
description: Flag to output optional file with final mask of non-gap RF len
|
||
|
|
|
||
|
|
- fmask_all:
|
||
|
|
type: val
|
||
|
|
description: Flag to output optional file with final mask of full aln len
|
||
|
|
|
||
|
|
- gmask_rf:
|
||
|
|
type: val
|
||
|
|
description: Flag to output optional file gap-based 0/1 mask of non-gap RF len
|
||
|
|
|
||
|
|
- gmask_all:
|
||
|
|
type: val
|
||
|
|
description: Flag to output optional file gap-based 0/1 mask of full aln len
|
||
|
|
|
||
|
|
- pmask_rf:
|
||
|
|
type: val
|
||
|
|
description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len
|
||
|
|
|
||
|
|
- pmask_all:
|
||
|
|
type: val
|
||
|
|
description: Flag to output optional file with PP-based 0/1 mask of full aln len
|
||
|
|
|
||
|
|
- maskfile:
|
||
|
|
type: file
|
||
|
|
description: mask file, see program documentation
|
||
|
|
pattern: "*"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
|
||
|
|
- maskedaln:
|
||
|
|
type: file
|
||
|
|
description: Masked alignment in gzipped Stockholm format
|
||
|
|
pattern: "*.sthlm.gz"
|
||
|
|
|
||
|
|
- fmask_rf:
|
||
|
|
type: file
|
||
|
|
description: File with final mask of non-gap RF len
|
||
|
|
pattern: "*.fmask-rf.gz"
|
||
|
|
|
||
|
|
- fmask_all:
|
||
|
|
type: file
|
||
|
|
description: File with final mask of full aln len
|
||
|
|
pattern: "*.fmask-all.gz"
|
||
|
|
|
||
|
|
- gmask_rf:
|
||
|
|
type: file
|
||
|
|
description: File with gap-based 0/1 mask of non-gap RF len
|
||
|
|
pattern: "*.gmask-rf.gz"
|
||
|
|
|
||
|
|
- gmask_all:
|
||
|
|
type: file
|
||
|
|
description: File with gap-based 0/1 mask of full aln len
|
||
|
|
pattern: "*.gmask-all.gz"
|
||
|
|
|
||
|
|
- pmask_rf:
|
||
|
|
type: file
|
||
|
|
description: File with PP-based 0/1 mask of non-gap RF len
|
||
|
|
pattern: "*.pmask-rf.gz"
|
||
|
|
|
||
|
|
- pmask_all:
|
||
|
|
type: file
|
||
|
|
description: File with PP-based 0/1 mask of full aln len
|
||
|
|
pattern: "*.pmask-all.gz"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@erikrikarddaniel"
|