definition.yml

method:
  id: scoup
  name: SCOUP
  tool_id: scoup
  source: tool
  platform: C++
  url: https://github.com/hmatsu1226/SCOUP
  license: MIT
  authors:
  - given: Hirotaka
    family: Matsumoto
    email: hirotaka.matsumoto@riken.jp
    github: hmatsu1226

manuscript:
  doi: 10.1186/s12859-016-1109-3
  google_scholar_cluster_id: '16676054631565429360'
  publication_date: '2016-06-08'

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

wrapper:
  type: end_state_probabilities
  topology_inference: parameter
  trajectory_types:
  - linear
  - bifurcation
  - multifurcation
  input_required:
  - expression
  - groups_id
  - start_id
  - end_n

parameters:
  - id: ndim
    type: integer
    default: 2
    distribution:
      type: uniform
      upper: 20
      lower: 2
    description: Number of pca dimensions
  - id: max_ite1
    type: integer
    default: 100
    distribution:
      type: expuniform
      upper: 5000
      lower: 2
    description: Upper bound of EM iteration (without pseudo-time optimization).
  - id: max_ite2
    type: integer
    default: 100
    distribution:
      type: expuniform
      upper: 500000
      lower: 2
    description: Upper bound of EM iteration (including pseudo-time optimization).
  - id: alpha
    type: numeric_range
    default:
    - 0.1
    - 100.0
    upper_distribution:
      type: expuniform
      lower: 0.001
      upper: 10.0
    lower_distribution:
      type: expuniform
      lower: 0.001
      upper: 10.0
    description: Bounds of alpha.
  - id: t
    type: numeric_range
    default:
    - 0.001
    - 2.0
    upper_distribution:
      type: expuniform
      lower: 1.0e-05
      upper: 1.0
    lower_distribution:
      type: expuniform
      lower: 1.0e-05
      upper: 1.0
    description: Bounds of pseudo-time.
  - id: sigma_squared
    type: numeric
    default: 0.1
    distribution:
      type: expuniform
      upper: 10.0
      lower: 0.001
    description: Lower bound of sigma squared
  - id: thresh
    type: numeric
    default: 0.01
    distribution:
      type: expuniform
      upper: 10.0
      lower: 0.01
    description: Threshold