---
slivka-version: 0.8.3
name: ClustalO
description: Clustal Omega is the latest addition to the Clustal family.
  It offers a significant increase in scalability over previous versions,
  allowing hundreds of thousands of sequences to be aligned in only 
  a few hours. It will also make use of multiple processors, where present. 
  In addition, the quality of alignments is superior to previous versions, 
  as measured by a range of popular benchmarks. 
author: Fabian Sievers, Andreas Wilm, David Dineen, Johannes Söding,
  Michael Remmert
version: '1.2.4'
license: GNU GPL ver. 2

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

parameters:
  input:
    name: Input file
    type: file
    required: true
#    max-size: 4MB
    media-type: application/fasta

  dealign:
    name: Dealign
    description: Dealign input sequences
    type: boolean
    default: false
    required: false

  full-distance:
    name: Full distance matrix
    description: Use full distance matrix for guide-tree calculation (slow;
      mBed is default)
    type: boolean
    default: false
    required: false

  full-distance-iteration:
    name: Full distance matrix for each iteration
    description: Use full distance matrix for guide-tree calculation during
      iteration (mBed is default)
    type: boolean
    default: false
    required: false

  max-hmm-iterations:
    name: Max Guide tree iterations
    description: Maximum number of HMM iterations
    type: int
    min: 1
    max: 100
    default: 1

  iterations:
    name: Number of iterations (combined)
    description: Number of (combined guide tree/HMM) iterations
    type: int
    min: 1
    max: 100
    default: 1

  max-guidetree-iterations:
    name: Max Guide tree iterations
    description: Maximum guide tree iterations
    type: int
    min: 1
    max: 100
    default: 1

command:
- clustalo

args:
  input:
    arg: --infile=$(value)
    symlink: input.txt
  dealign:
    arg: --dealign
  full-distance:
    arg: --full
  full-distance-iteration:
    arg: --full-iter
  max-hmm-iterations:
    arg: --max-hmm-iterations=$(value)
  iterations:
    arg: --iter=$(value)
  max-guidetree-iterations:
    arg: --max-guidetree-iterations=$(value)
  _const0:
    arg: --outfile=output.txt
    default: present
  _const1:
    arg: --outfmt=clustal
    default: present
  _const2:
    arg: -v
    default: present
  _const3:
    arg: --log=stat.log
    default: present
  _const4:
    arg: --threads=1
    default: present
    
outputs:
  alignment:
    path: output.txt
    media-type: application/clustal
  tree:
    path: input.dnd
  log:
    path: stat.log
    media-type: text/plain
  error-log:
    path: stderr
    media-type: text/plain

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

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