Exemplos de run_cwltool em Python

Exemplo n.º 1

Arquivo: cmd_cwl_run.py Projeto: einon/planemo

def cli(ctx, path, job_path, **kwds):
    """Planemo command for running CWL tools and jobs.

    ::

        % planemo cwl_run cat1-tool.cwl cat-job.json
    """
    engine = kwds.get("cwl_engine", "galaxy")
    if engine == "galaxy":
        return cwl.run_galaxy(ctx, path, job_path, **kwds)
    else:
        return cwl.run_cwltool(ctx, path, job_path, **kwds)

Exemplo n.º 2

def cli(ctx, path, job_path, **kwds):
    """Planemo command for running CWL tools and jobs.

    ::

        % planemo cwl_run cat1-tool.cwl cat-job.json
    """
    engine = kwds.get("cwl_engine", "galaxy")
    if engine == "galaxy":
        return cwl.run_galaxy(ctx, path, job_path, **kwds)
    else:
        return cwl.run_cwltool(ctx, path, job_path, **kwds)

Exemplo n.º 3

 def _run(self, runnable, job_path):
     """Run CWL job using cwltool."""
     return cwl.run_cwltool(self._ctx, runnable, job_path, **self._kwds)

Exemplo n.º 4

Arquivo: cwltool.py Projeto: galaxyproject/planemo

 def _run(self, runnable, job_path):
     """Run CWL job using cwltool."""
     path = runnable.path
     return cwl.run_cwltool(self._ctx, path, job_path, **self._kwds)