definition.yml

method:
  id: mpath
  name: Mpath
  tool_id: mpath
  source: tool
  platform: R
  url: https://github.com/JinmiaoChenLab/Mpath
  authors:
  - given: Michael
    family: Poidinger
    email: michael_poidinger@immunol.a-star.edu.sg
    ORCID: 0000-0002-1047-2277
  - given: Jinmiao
    family: Chen
    email: chen_jinmiao@immunol.a-star.edu.sg
    github: jinmiaochen
    ORCID: 0000-0001-7547-6423


manuscript:
  doi: 10.1038/ncomms11988
  google_scholar_cluster_id: '13279740541516941155'
  publication_date: '2016-06-30'

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

wrapper:
  type: cluster_graph
  topology_inference: free
  trajectory_types:
  - linear
  - bifurcation
  - multifurcation
  - tree
  input_required:
  - counts
  - groups_id


parameters:
  - id: distMethod
    type: character
    default: euclidean
    values:
    - pearson
    - kendall
    - spearman
    - euclidean
    description: the method for calculating dissimilarity between cells. distMethod
      can be one of "pearson", "kendall", "spearman" or "euclidean". Default is "euclidean".
  - id: method
    type: character
    default: kmeans
    values:
    - kmeans
    - diversity
    - size
    - diversity_size
    description: method for distinguishing landmark clusters from non-landmark clusters.method
      can be "kmeans" or "diversity" or "size" or "diversity_size". When method="diversity",
      numlm needs to be specified. Default is "diversity_size".
  - id: numcluster
    type: integer
    default: 11
    distribution:
      type: uniform
      upper: 30
      lower: 3
    description: number of initial clusters
  - id: numcluster_null
    type: logical
    default: yes
    description: If TRUE, will automatically select the number of clusters
  - id: diversity_cut
    type: numeric
    default: 0.6
    distribution:
      type: uniform
      upper: 1.0
      lower: 0.1
    description: the cutoff value of diversity for differentiating landmark clusters
      from non-landmark clusters. The diversity of a landmark cluster must be below
      this cutoff.
  - id: size_cut
    type: numeric
    default: 0.05
    distribution:
      type: uniform
      upper: 1.0
      lower: 0.01
    description: the cutoff value of size i.e. number of cells for differentiating
      landmark clusters from non-landmark clusters. The number of cells in a landmark
      cluster must be greater than this cutoff.