--- a/env/lib/python3.7/site-packages/planemo/commands/cmd_run.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-"""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