Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/planemo/commands/cmd_run.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
|---|---|
| date | Sat, 02 May 2020 07:14:21 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/planemo/commands/cmd_run.py Sat May 02 07:14:21 2020 -0400 @@ -0,0 +1,54 @@ +"""Module describing the planemo ``cwl_run`` command.""" +from __future__ import print_function + +import json + +import click +from galaxy.util import unicodify + +from planemo import options +from planemo.cli import command_function +from planemo.engine import engine_context +from planemo.io import warn +from planemo.tools import uri_to_path + + +@click.command('run') +@options.required_tool_arg(allow_uris=True) +@options.required_job_arg() +@options.galaxy_run_options() +@options.galaxy_config_options() +@options.enable_cwl_option() +@options.galaxy_cwl_root_option() +@options.run_output_directory_option() +@options.run_output_json_option() +@options.engine_options() +@command_function +def cli(ctx, uri, job_path, **kwds): + """Planemo command for running tools and jobs. + + \b + % planemo run cat1-tool.cwl cat-job.json + """ + path = uri_to_path(ctx, uri) + # TODO: convert UI to runnable and do a better test of cwl. + is_cwl = path.endswith(".cwl") + kwds["cwl"] = is_cwl + if kwds.get("engine", None) is None: + kwds["engine"] = "galaxy" if not is_cwl else "cwltool" + + with engine_context(ctx, **kwds) as engine: + run_result = engine.run(path, job_path) + + if not run_result.was_successful: + warn("Run failed [%s]" % unicodify(run_result)) + ctx.exit(1) + + outputs_dict = run_result.outputs_dict + print(outputs_dict) + output_json = kwds.get("output_json", None) + if output_json: + with open(output_json, "w") as f: + json.dump(outputs_dict, f) + + return 0