{% set version = "1.8.0" %}
{% set name = "pbcmc" %}
{% set bioc = "3.7" %}

package:
  name: 'bioconductor-{{ name|lower }}'
  version: '{{ version }}'
source:
  url:
    - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
  sha256: 8a8cab9b7217dcaca40bbf039aa808f74e3e66d992fcb69060fbfaf4bb287073
build:
  number: 0
  rpaths:
    - lib/R/lib/
    - lib/
requirements:
  host:
    - 'bioconductor-biobase >=2.40.0,<2.42.0'
    - 'bioconductor-biocgenerics >=0.26.0,<0.28.0'
    - 'bioconductor-biocparallel >=1.14.2,<1.16.0'
    - 'bioconductor-genefu >=2.12.0,<2.14.0'
    - 'bioconductor-limma >=3.36.5,<3.38.0'
    - r-base
    - r-cowplot
    - r-ggplot2
    - r-gridextra
    - r-reshape2
  run:
    - 'bioconductor-biobase >=2.40.0,<2.42.0'
    - 'bioconductor-biocgenerics >=0.26.0,<0.28.0'
    - 'bioconductor-biocparallel >=1.14.2,<1.16.0'
    - 'bioconductor-genefu >=2.12.0,<2.14.0'
    - 'bioconductor-limma >=3.36.5,<3.38.0'
    - r-base
    - r-cowplot
    - r-ggplot2
    - r-gridextra
    - r-reshape2
test:
  commands:
    - '$R -e "library(''{{ name }}'')"'
about:
  home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
  license: 'GPL (>=2)'
  summary: 'The pbcmc package characterizes uncertainty assessment on gene expression classifiers, a. k. a. molecular signatures, based on a permutation test. In order to achieve this goal, synthetic simulated subjects are obtained by permutations of gene labels. Then, each synthetic subject is tested against the corresponding subtype classifier to build the null distribution. Thus, classification confidence measurement can be provided for each subject, to assist physician therapy choice. At present, it is only available for PAM50 implementation in genefu package but it can easily be extend to other molecular signatures.'
extra:
  identifiers:
    - biotools:pbcmc
    - doi:10.1038/nmeth.3252
