definition.yml

method:
  id: celltree_vem
  name: cellTree vem
  tool_id: celltree
  source: tool
  platform: R
  url: https://bioconductor.org/packages/release/bioc/html/cellTree.html
  license: Artistic-2.0
  authors:
  - given: David
    family: duVerle
    email: dave@cb.k.u-tokyo.ac.jp
    ORCID: 0000-0003-2836-0502
    github: david-duverle
  - given: Koji
    family: Tsuda
    email: tsuda@k.u-tokyo.ac.jp
    ORCID: 0000-0002-4288-1606
    github: tsudalab

manuscript:
  doi: 10.1186/s12859-016-1175-6
  google_scholar_cluster_id: '6029217784505101308'
  publication_date: '2016-08-13'

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

wrapper:
  type: cell_graph
  topology_inference: free
  trajectory_types:
  - linear
  - bifurcation
  - convergence
  - multifurcation
  - binary_tree
  - tree
  input_required: expression
  input_optional:
  - start_id
  - groups_id

parameters:
  - id: method
    description: 'LDA inference method to use.'
    type: character
    default: VEM
    values: VEM
  - id: sd_filter
    description: 'Standard-deviation threshold below which genes should be removed from the data.'
    type: numeric
    default: 0.5
    distribution:
      type: expuniform
      lower: 0.01
      upper: 5.0
  - id: width_scale_factor
    description: 'A scaling factor for the dynamically-computed distance threshold (ignored if absolute_width is provided). Higher values will result in less branches in the backbone tree, while lower values might lead to a large number of backbone branches.'
    type: numeric
    default: 1.5
    distribution:
      type: expuniform
      lower: 0.1
      upper: 100
  - id: outlier_tolerance_factor
    description: 'Proportion of vertices, out of the total number of vertices divided by the total number of branches, that can be left at the end of the backbone tree-building algorithm.'
    type: numeric
    default: 0.1
    distribution:
      type: expuniform
      lower: 0.0001
      upper: 1000
  - id: rooting_method
    description: 'Method used to root the backbone tree. Must be either NULL or one of ‘longest.path’, ‘center.start.group’ or ‘average.start.group’. ‘longest.path’ picks one end of the longest shortest-path between two vertices. ’center.start.group’ picks the vertex in the starting group with lowest mean-square-distance to the others. ‘average.start.group’ creates a new artificial vertex, as the average of all cells in the starting group. If no value is provided, the best method is picked based on the type of grouping and start group information available.'
    type: character
    values:
    - longest.path
    - center.start.group
    - average.start.group
    - 'null'
    default: 'null'
  - id: num_topics
    description: 'Number of topics to fit in the model.'
    type: integer
    default: 4
    distribution:
      type: uniform
      lower: 2
      upper: 15
  - id: tot_iter
    description: "Numeric parameters (optional) forwarded to the chosen LDA inference method's contol class."
    type: numeric
    default: 1000000
    distribution:
      type: expuniform
      lower: 10000
      upper: 10000000
  - id: tolerance
    description: "Numeric parameters (optional) forwarded to the chosen LDA inference method's contol class."
    type: numeric
    default: 1.0e-05
    distribution:
      type: expuniform
      lower: 1.0e-07
      upper: 0.001