method:
  id: scorpius
  name: SCORPIUS
  tool_id: scorpius
  source: tool
  platform: R
  url: https://github.com/rcannood/SCORPIUS
  license: GPL-3
  authors:
  - given: Robrecht
    family: Cannoodt
    email: rcannood@gmail.com
    ORCID: 0000-0003-3641-729X
    github: rcannood
  - given: Wouter
    family: Saelens
    email: wouter.saelens@ugent.be
    ORCID: 0000-0002-7114-6248
    github: zouter
  - given: Yvan
    family: Saeys
    email: yvan.saeys@ugent.be
    github: saeyslab


manuscript:
  doi: 10.1101/079509
  google_scholar_cluster_id: '7752629025700865018'
  preprint_date: '2016-10-07'

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

package:
  remote: rcannood/SCORPIUS
  name: SCORPIUS
  function_name: ti_scorpius

wrapper:
  type: linear_trajectory
  topology_inference: fixed
  trajectory_types: linear
  input_required: expression
  input_optional: dimred

parameters:
  - id: distance_method
    type: character
    default: spearman
    values:
    - spearman
    - pearson
    - cosine
    description: |-
      A character string indicating which correlation
      coefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine".
  - id: ndim
    type: integer
    default: 3
    distribution:
      type: uniform
      upper: 20
      lower: 2
    description: The number of dimensions in the new space.
  - id: k
    type: integer
    default: 4
    distribution:
      type: uniform
      upper: 20
      lower: 1
    description: The number of clusters to cluster the data into to construct the initial trajectory.
  - id: thresh
    type: numeric
    default: 0.001
    distribution:
      type: expuniform
      upper: 100000
      lower: 1.0e-05
    description: '`principal_curve` parameter; convergence threshhold on shortest distances to the curve'
  - id: maxit
    type: integer
    default: 10
    distribution:
      type: uniform
      upper: 50
      lower: 0
    description: '`principal_curve` parameter; maximum number of iterations'
  - id: stretch
    type: numeric
    default: 0.0
    distribution:
      type: uniform
      upper: 5.0
      lower: 0.0
    description: '`principal_curve` parameter; a factor by which the curve can be extrapolated when points are projected'
  - id: smoother
    type: character
    default: smooth_spline
    values:
    - smooth_spline
    - lowess
    - periodic_lowess
    description: '`principal_curve` parameter; choice of smoother'
