Implement non-strict CWL parsing option.

For cwltool and Galaxy engines.

Author: jmchilton

planemo/cwl/run.py

@@ -71,7 +71,8 @@ def run_cwltool(ctx, path, job_path, **kwds):
     if kwds.get("no_container", False):
         args.append("--no-container")
 
-    args.append("--non-strict")
+    if kwds.get("non_strict_cwl", False):
+        args.append("--non-strict")
 
     args.extend([path, job_path])
     ctx.vlog("Calling cwltool with arguments %s" % args)

planemo/galaxy/config.py

@@ -536,6 +536,7 @@ def _shared_galaxy_properties(config_directory, kwds, for_tests):
         'check_migrate_tools': "False",
         'use_cached_dependency_manager': str(kwds.get("conda_auto_install", False)),
         'brand': kwds.get("galaxy_brand", DEFAULT_GALAXY_BRAND),
+        'strict_cwl_validation': str(not kwds.get("non_strict_cwl", False)),
     }
     if for_tests:
         empty_dir = os.path.join(config_directory, "empty")

planemo/options.py

@@ -44,6 +44,15 @@ def run_engine_option():
     )
 
 
+def non_strict_cwl_option():
+    return planemo_option(
+        "--non_strict_cwl",
+        default=False,
+        is_flag=True,
+        help="Disable strict validation of CWL.",
+    )
+
+
 def serve_engine_option():
     return planemo_option(
         "--engine",
@@ -992,6 +1001,7 @@ def galaxy_serve_options():
     return _compose(
         galaxy_run_options(),
         serve_engine_option(),
+        non_strict_cwl_option(),
         docker_galaxy_image_option(),
         galaxy_config_options(),
         daemon_option(),
@@ -1086,6 +1096,7 @@ def tool_test_json():
 def engine_options():
     return _compose(
         run_engine_option(),
+        non_strict_cwl_option(),
         cwltool_no_container_option(),
         docker_galaxy_image_option(),
     )