#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow inputs: rulesfile: File sourcefile: File sinkfile: File reverse: boolean max-steps: int? outputs: compounds: type: File outputSource: rp2paths/compounds reactions: type: File outputSource: rp2paths/reactions sinks: type: File outputSource: rp2paths/sinks steps: rp2: run: ../tools/RetroPath2/RetroPath2.cwl in: input.rulesfile: rulesfile input.sourcefile: sourcefile input.sinkfile: sinkfile input.max-steps: max-steps out: [solutionfile] rp2paths: run: ../tools/rp2paths/rp2paths.cwl in: infile: rp2/solutionfile reverse: reverse out: [compounds, reactions, sinks] hints: dep:Dependencies: dependencies: - upstream: https://raw.githubusercontent.com/ibisba/RetroPath2-cwl/0.0.1/tools/RetroPath2.cwl installTo: ../tools/RetroPath2 - upstream: https://raw.githubusercontent.com/ibisba/rp2paths-cwl/1.0.2-1/tools/rp2paths.cwl installTo: ../tools/rp2paths $namespaces: dep: http://commonwl.org/cwldep#