--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/planemo/cwl/toil.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,80 @@
+from __future__ import absolute_import
+
+import json
+import tempfile
+
+try:
+    from toil.cwl import cwltoil
+except ImportError:
+    cwltoil = None
+
+from planemo.deps import ensure_dependency_resolvers_conf_configured
+from planemo.io import error, real_io
+from planemo.runnable import (
+    ErrorRunResponse,
+)
+from .run import (
+    CwlToolRunResponse,
+    JSON_PARSE_ERROR_MESSAGE
+)
+
+
+TOIL_REQUIRED_MESSAGE = "This functionality requires Toil, please install with 'pip install toil'"
+
+
+def run_toil(ctx, path, job_path, **kwds):
+    """Translate planemo kwds to cwltool kwds and run cwltool main function."""
+    _ensure_toil_available()
+
+    args = []
+    if not ctx.verbose:
+        args.append("--quiet")
+    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 cwltoil with arguments %s" % args)
+    with tempfile.NamedTemporaryFile("w") as tmp_stdout:
+        # cwltool passes sys.stderr to subprocess.Popen - ensure it has
+        # and actual fileno.
+        with real_io():
+            ret_code = cwltoil.main(
+                args,
+                stdout=tmp_stdout
+            )
+        tmp_stdout.flush()
+        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,
+                )
+                error(message)
+                raise Exception(message)
+
+        if ret_code != 0:
+            return ErrorRunResponse("Error running Toil")
+        outputs = result
+    return CwlToolRunResponse(
+        "",
+        outputs=outputs,
+    )
+
+
+def _ensure_toil_available():
+    if cwltoil is None:
+        raise Exception(TOIL_REQUIRED_MESSAGE)