Add --cwl_engine argument to cwl_run.

Allow running the reference implementation using planemo.

Author: jmchilton

planemo/commands/cmd_cwl_run.py

@@ -26,4 +26,8 @@ def cli(ctx, path, job_path, **kwds):
 
         % planemo cwl_run cat1-tool.cwl cat-job.json
     """
-    return cwl.run_galaxy(ctx, path, job_path, **kwds)
+    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)

planemo/cwl/__init__.py

@@ -1,5 +1,6 @@
-from .client import run_cwl_tool
+from .run import run_galaxy, run_cwltool
 
 __all__ = [
-    'run_cwl_tool',
+    'run_galaxy',
+    'run_cwltool',
 ]

planemo/cwl/run.py

@@ -1,3 +1,9 @@
+from planemo.io import conditionally_captured_io
+from planemo import galaxy_serve
+from .client import run_cwl_tool
+from planemo import io
+
+from cwltool.main import main
 
 
 def run_galaxy(ctx, path, job_path, **kwds):
@@ -6,11 +12,23 @@ def run_galaxy(ctx, path, job_path, **kwds):
     with conditionally_captured_io(conformance_test):
         with galaxy_serve.serve_daemon(ctx, [path], **kwds) as config:
             try:
-                cwl_run = cwl.run_cwl_tool(path, job_path, config, **kwds)
+                cwl_run = run_cwl_tool(path, job_path, config, **kwds)
             except Exception:
                 io.warn("Problem running cwl tool...")
                 print(config.log_contents)
                 raise
 
     print(cwl_run.cwl_command_state)
     return 0
+
+
+def run_cwltool(ctx, path, job_path, **kwds):
+    args = []
+    if kwds.get("conformance_test", False):
+        args.append("--conformance-test")
+    if ctx.verbose:
+        args.append("--verbose")
+
+    args.extend([path, job_path])
+    ctx.vlog("Calling cwltool with arguments %s" % args)
+    return main(args)