Fix workflow init metadata handling

Author: jmchilton

planemo/commands/cmd_workflow_job_init.py

@@ -60,6 +60,8 @@ def _build_commented_yaml(job, metadata):
             if collection_type:
                 comment_parts.append(f"collection_type: {collection_type}")
             if input_format:
+                if isinstance(input_format, list):
+                    input_format = ", ".join(input_format)
                 comment_parts.append(f"format: {input_format}")
             if input_doc:
                 comment_parts.append(f"doc: {input_doc}")

planemo/galaxy/workflows.py

@@ -685,7 +685,7 @@ def job_template(workflow_path, **kwds):
                     }
                 ],
             }
-        elif input_type in ["string", "int", "float", "boolean", "color"]:
+        elif input_type in ["string", "int", "integer", "float", "boolean", "color"]:
             template[i_label] = "todo_param_value"
         else:
             template[i_label] = {
@@ -785,7 +785,7 @@ def _build_template_and_metadata_from_inputs(
                 "collection_type": coll_type,
                 "elements": _collection_elements_for_type(coll_type),
             }
-        elif input_type in ["string", "int", "float", "boolean", "color"]:
+        elif input_type in ["string", "int", "integer", "float", "boolean", "color"]:
             # Use default value if available, otherwise use placeholder or false for booleans
             if has_default:
                 template[i_label] = default_value

tests/data/wf14-unlinted-best-practices.yml

@@ -2,7 +2,7 @@ class: GalaxyWorkflow
 label: bp (imported from uploaded file)
 uuid: 66708ffe-c08c-4647-a7e9-fc7f731206a1
 inputs:
-  null:
+  input1:
     optional: false
     position:
       bottom: 730.3166656494141