---
slivka-version: 0.8.3
name: MUSCLE
description: MUSCLE is one of the best-performing multiple alignment 
  programs according to published benchmark tests, with accuracy and 
  speed that are consistently better than CLUSTALW. MUSCLE can align 
  hundreds of sequences in seconds. Most users learn everything they 
  need to know about MUSCLE in a few minutes—only a handful of 
  command-line options are needed to perform common alignment tasks.
author: Robert C. Edgar
version: '5.1'
license: Public Domain

classifiers:
- 'Topic :: Computational biology :: Sequence analysis'
- 'Operation :: Analysis :: Sequence analysis :: Sequence alignment ::
  Multiple sequence alignment'

command:
- muscle

args:
  algorithm:
    arg: -$(value)
  input:
    arg: $(value)
  _output:
    arg: -output $(value)
    default: aln.afa
  perturb:
    arg: -perturb $(value)
  perm:
    arg: -perm $(value)
  consiters:
    arg: -consiters $(value)
  refineiters:
    arg: -refineiters $(value)
  threads:
    arg: -threads $(value)

parameters:
  input:
    name: Input sequences
    type: file
    required: true
  
  algorithm:
    name: Align algorithm
    type: choice
    choices:
      PPP: align
      Super5: super5
    required: true
    default: PPP

  perturb:
    name: HMM perturbations seed
    description: An integer number used as a random generator seed
      for generating HMM perturbations.
    type: int
    required: false
    default: 0
  
  perm:
    name: Guide tree permutation
    type: choice
    choices:
      none: none
      abc: abc
      acb: acb
      bca: bca
    required: false
    default: none

  consiters:
    name: Consistency iterations
    type: int
    required: false
    default: 2

  refineiters:
    name: Refinement iterations
    type: int
    required: false
    default: 100

outputs:
  alignment:
    path: aln.afa
    media-type: application/fasta
  log:
    path: stdout
    media-type: text/plain
  error-log:
    path: stderr
    media-type: text/plain

tests:
- applicable-runners: ["default"]
  parameters:
    input: "{{ local-path:testdata }}/uniref50.fa"
    algorithm: align
    _output: aln.fa
  timeout: 60

execution:
  runners:
    default: !include _profiles.yaml::default
...