mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
57 lines
2 KiB
YAML
57 lines
2 KiB
YAML
|
name: muscle
|
||
|
|
description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two
|
||
|
|
keywords:
|
||
|
|
- msa
|
||
|
|
- multiple sequence alignment
|
||
|
|
tools:
|
||
|
|
- muscle:
|
||
|
|
description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput
|
||
|
|
homepage: https://www.drive5.com/muscle
|
||
|
|
documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840
|
||
|
|
doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/"
|
||
|
|
licence: ['http://www.drive5.com/muscle/manual/license.html']
|
||
|
|
input:
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: Input sequences for alignment must be in FASTA format
|
||
|
|
pattern: "*.{fasta,fa,fna}"
|
||
|
|
output:
|
||
|
|
- aligned_fasta:
|
||
|
|
type: file
|
||
|
|
description: Multiple sequence alignment produced in FASTA format
|
||
|
|
pattern: "*.{afa}"
|
||
|
|
- msf:
|
||
|
|
type: file
|
||
|
|
description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW)
|
||
|
|
pattern: "*.{msf}"
|
||
|
|
- clustalw:
|
||
|
|
type: file
|
||
|
|
description: Multiple sequence alignment produced in ClustalW format without base/residue numbering
|
||
|
|
pattern: "*.{clw}"
|
||
|
|
- phyi:
|
||
|
|
type: file
|
||
|
|
description: Multiple sequence alignment produced in PHYLIP interleaved format
|
||
|
|
pattern: "*.{phyi}"
|
||
|
|
- phys:
|
||
|
|
type: file
|
||
|
|
description: Multiple sequence alignment produced in PHYLIP sequential format
|
||
|
|
pattern: "*.{phys}"
|
||
|
|
- html:
|
||
|
|
type: file
|
||
|
|
description: Multiple sequence alignment produced in HTML format
|
||
|
|
pattern: "*.{html}"
|
||
|
|
- tree:
|
||
|
|
type: file
|
||
|
|
description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment
|
||
|
|
pattern: "*.{tree}"
|
||
|
|
- log:
|
||
|
|
type: file
|
||
|
|
description: Log file of MUSCLE run
|
||
|
|
pattern: "*{.log}"
|
||
|
|
- version:
|
||
|
|
type: file
|
||
|
|
description: File containing MUSCLE software version
|
||
|
|
pattern: "*.{version.txt}"
|
||
|
|
authors:
|
||
|
|
- "@MGordon"
|