--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/planemo/cwl/run.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,108 @@
+"""Module defines a planemo abstraction around running cwltool.
+
+cwltool is an executable Python script and library mostly maintained by
+Peter Amstutz and serves the reference implementation for the CWL.
+It can be found at https://github.com/common-workflow-language/cwltool,
+"""
+import json
+import tempfile
+
+from galaxy.tool_util.cwl.cwltool_deps import (
+    ensure_cwltool_available,
+    main,
+)
+
+from planemo.deps import ensure_dependency_resolvers_conf_configured
+from planemo.io import error, real_io
+from planemo.runnable import (
+    ErrorRunResponse,
+    SuccessfulRunResponse,
+)
+
+JSON_PARSE_ERROR_MESSAGE = ("Failed to parse JSON from cwltool output [%s] "
+                            "in file [%s]. cwltool logs [%s].")
+
+
+class CwlToolRunResponse(SuccessfulRunResponse):
+    """Describe the resut of a cwltool invocation."""
+
+    def __init__(self, log, outputs=None):
+        self._log = log
+        self._outputs = outputs
+
+    @property
+    def log(self):
+        return self._log
+
+    @property
+    def job_info(self):
+        return None
+
+    @property
+    def outputs_dict(self):
+        return self._outputs
+
+
+def run_cwltool(ctx, path, job_path, **kwds):
+    """Translate planemo kwds to cwltool kwds and run cwltool main function."""
+    ensure_cwltool_available()
+
+    args = []
+    if ctx.verbose:
+        args.append("--verbose")
+    output_directory = kwds.get("output_directory", None)
+    if output_directory:
+        args.append("--outdir")
+        args.append(output_directory)
+    if kwds.get("no_container", False):
+        args.append("--no-container")
+        ensure_dependency_resolvers_conf_configured(ctx, kwds)
+        args.append("--beta-dependency-resolvers-configuration")
+        args.append(kwds["dependency_resolvers_config_file"])
+    if kwds.get("mulled_containers"):
+        args.append("--beta-use-biocontainers")
+
+    if kwds.get("non_strict_cwl", False):
+        args.append("--non-strict")
+
+    args.extend([path, job_path])
+    ctx.vlog("Calling cwltool with arguments %s" % args)
+    with tempfile.NamedTemporaryFile("w") as tmp_stdout, \
+            tempfile.NamedTemporaryFile("w") as tmp_stderr:
+        # cwltool passes sys.stderr to subprocess.Popen - ensure it has
+        # and actual fileno.
+        with real_io():
+            ret_code = main.main(
+                args,
+                stdout=tmp_stdout,
+                stderr=tmp_stderr,
+            )
+        tmp_stdout.flush()
+        tmp_stderr.flush()
+        with open(tmp_stderr.name, "r") as stderr_f:
+            log = stderr_f.read()
+            ctx.vlog("cwltool log output [%s]" % log)
+        with open(tmp_stdout.name, "r") as stdout_f:
+            try:
+                result = json.load(stdout_f)
+            except ValueError:
+                message = JSON_PARSE_ERROR_MESSAGE % (
+                    open(tmp_stdout.name, "r").read(),
+                    tmp_stdout.name,
+                    log
+                )
+                error(message)
+                raise Exception(message)
+
+        if ret_code != 0:
+            return ErrorRunResponse("Error running cwltool", log=log)
+        outputs = result
+    return CwlToolRunResponse(
+        log,
+        outputs=outputs,
+    )
+
+
+__all__ = (
+    "run_cwltool",
+)