cwl/lightning/lightning-plot.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7 cwlVersion: v1.2
   8 class: CommandLineTool
   9 requirements:
  10   NetworkAccess:
  11     networkAccess: true
  12 hints:
  13   DockerRequirement:
  14     dockerPull: lightning
  15   ResourceRequirement:
  16     coresMin: 2
  17     ramMin: 10000
  18   arv:RuntimeConstraints:
  19     keep_cache: 20000
  20     outputDirType: keep_output_dir
  21 inputs:
  22   pcanpy: File
  23   pcasamplescsv: File
  24   phenotypesdir: Directory
  25   xcomponent: string
  26   ycomponent: string
  27 outputs:
  28   png:
  29     type: File
  30     outputBinding:
  31       glob: "*.png"
  32 baseCommand: [lightning, plot]
  33 arguments:
  34   - "-local=true"
  35   - prefix: "-i="
  36     valueFrom: $(inputs.pcanpy)
  37     separate: false
  38   - prefix: "-o="
  39     valueFrom: "plot_$(inputs.xcomponent)-$(inputs.ycomponent).png"
  40     separate: false
  41   - prefix: "-samples="
  42     valueFrom: $(inputs.pcasamplescsv)
  43     separate: false
  44   - prefix: "-phenotype="
  45     valueFrom: $(inputs.phenotypesdir)
  46     separate: false
  47   - "-phenotype-cat1-column=7"
  48   - prefix: "-x="
  49     valueFrom: $(inputs.xcomponent)
  50     separate: false
  51   - prefix: "-y="
  52     valueFrom: $(inputs.ycomponent)
  53     separate: false