definition.yml

method:
  id: elpigraph
  name: ElPiGraph
  source: tool
  tool_id: elpigraph
  platform: R
  url: https://github.com/Albluca/ElPiGraph.R
  license: GPL-3
  authors:
  - given: Luca
    family: Albergante
    email: luca.albergante@gmail.com
    github: Albluca
    ORCID: 0000-0001-8151-6989

manuscript:
  google_scholar_cluster_id: '13755708560339919612'
  preprint_date: '2018-04-20'

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

wrapper:
  type: trajectory
  topology_inference: free
  trajectory_types:
  - linear
  - bifurcation
  - convergence
  - multifurcation
  - binary_tree
  - tree
  input_required:
  - expression

parameters:
  - id: topology
    description: the kind of topology to detect
    type: character
    values:
    - cycle
    - tree
    - linear
    default: tree
  - id: NumNodes
    description: the number of nodes of the principal graph
    type: integer
    distribution:
      type: uniform
      lower: 2
      upper: 1000
    default: 50
  - id: NumEdges
    description: the maximum number of edges
    type: integer
    distribution:
      type: expuniform
      lower: 2
      upper: 100000
    default: 100000
  - id: InitNodes
    description: number of points to include in the initial graph
    type: integer
    distribution:
      type: expuniform
      lower: 2
      upper: 1000
    default: 2
  - id: Mu
    description: controls the elastic energy
    type: numeric
    distribution:
      type: expuniform
      lower: 0.001
      upper: 1
    default: 0.1
  - id: Lambda
    description: controls the elastic energy
    type: numeric
    distribution:
      type: expuniform
      lower: 0.001
      upper: 1
    default: 0.01
  - id: MaxNumberOfIterations
    description: maximum number of steps to embed the nodes
    type: integer
    distribution:
      type: expuniform
      lower: 1
      upper: 1000
    default: 10
  - id: eps
    description: minimal relative change in the position of the nodes to stop embedment
    type: numeric
    distribution:
      type: expuniform
      lower: 0.001
      upper: 1
    default: 0.01
  - id: CenterData
    description: should data and initial node positions be centered?
    type: logical
    default: no