definition.yml

method:
  id: recat
  name: reCAT
  tool_id: recat
  source: tool
  platform: R
  url: https://github.com/tinglab/reCAT
  authors:
  - given: Riu
    family: Jian
    email: ruijiang@gmail.com
    github: louhzmaki

manuscript:
  doi: '10.1038/s41467-017-00039-z'
  google_scholar_cluster_id: '10600621261210432161'
  publication_date: '2017-06-19'

container:
  url: https://github.com/dynverse/ti_recat
  docker: dynverse/ti_recat

wrapper:
  type: cyclic_trajectory
  topology_inference: fixed
  trajectory_types: cycle
  input_required: expression

parameters:
  - id: TSPFold
    type: integer
    default: 2
    distribution:
      type: uniform
      upper: 10
      lower: 2
    description: No documentation provided by authors
  - id: beginNum
    type: integer
    default: 10
    distribution:
      type: uniform
      upper: 20
      lower: 2
    description: No documentation provided by authors
  - id: endNum
    type: integer
    default: 15
    distribution:
      type: uniform
      upper: 20
      lower: 2
    description: No documentation provided by authors
  - id: step_size
    type: integer
    default: 2
    distribution:
      type: uniform
      upper: 20
      lower: 2
    description: |-
      Determines the number of k to skip in your consensus path, ie if
      step_size = 2, then reCAT would only calculate and merge the paths for
      k = 12, 14, 16, 18, ..., n-2, n. We recommend step_size of up to a maximum of 5 while preserving the performance of reCAT. Usually a step_size of 2 (by default) would suffice and bigger steps are recommended for larger datasets (>1000 cells) in order to reduce computational time.
  - id: base_cycle_range
    type: integer_range
    default:
    - 6
    - 9
    lower_distribution:
      type: uniform
      lower: 5
      upper: 10
    upper_distribution:
      type: uniform
      lower: 5
      upper: 10
  - id: max_num
    type: integer
    default: 300
    distribution:
      type: uniform
      upper: 500
      lower: 100
    description: No documentation provided by authors
  - id: clustMethod
    type: character
    default: GMM
    values:
    - GMM
    - Pam
    - Kmeans
    description: No documentation provided by authors