{% set name = "pia" %}
{% set version = "1.5.1" %}
{% set sha256 = "46bd90546afc324246087552fa478c84b5e9dc324984109310ed46dbbd78412d" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

build:
  noarch: generic
  number: 0
  run_exports:
    - {{ pin_subpackage('pia', max_pin="x") }}

source:
  url: https://github.com/medbioinf/pia/releases/download/{{ version }}/pia-{{ version }}.zip
  sha256: {{ sha256 }}

requirements:
  run:
    - openjdk >=21

test:
  commands:
    - pia --help
    - pia -Xms512m -Xmx2g --help

about:
  home: https://github.com/medbioinf/pia
  license: BSD-3-Clause
  license_file: LICENSE
  summary: PIA is a toolbox for MS based protein inference and identification analysis.
  description: |
   PIA allows you to inspect the results of common proteomics spectrum identification
   search engines, combine them seamlessly and conduct statistical analyses. The main
   focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins
   from a set of identified spectra. But it also allows you to inspect your peptide
   spectrum matches, calculate FDR values across different search engine results and
   visualize the correspondence between PSMs, peptides and proteins.

extra: 
  identifiers:
    - biotools:pia
    - doi:10.1021/acs.jproteome.5b00121
  notes: |
    PIA is Java program that comes with a custom wrapper shell script.
    This shell wrapper is called "pia" and is on $PATH by default. By default
    "-Xms2g -Xmx4g" is set in the wrapper. If you want to overwrite it you can
    specify these values directly after your binaries. If you have _JAVA_OPTIONS
    set globally this will take precedence.
    For example run it with "pia -Xms512m -Xmx2g" for a lower memory footprint.
