convert: add dependency as mainEntity if it is the only one

Author: simleo

src/runcrate/convert.py

@@ -419,6 +419,8 @@ def add_tool(self, crate, workflow, cwl_tool):
         tool = crate.add(ContextEntity(crate, tool_id, properties=properties))
         if deps:
             tool["softwareRequirements"] = deps
+        if len(deps) == 1:
+            tool["mainEntity"] = deps[0]
         tool["input"] = self.add_params(crate, cwl_tool.inputs)
         tool["output"] = self.add_params(crate, cwl_tool.outputs)
         workflow.append_to("hasPart", tool)

tests/test_cwlprov_crate_builder.py

@@ -346,6 +346,7 @@ def test_dir_io(data_dir, tmpdir):
     assert grep.type == "SoftwareApplication"
     assert grep["name"] == "grep"
     assert grep["softwareVersion"] == ["3.8"]
+    assert greptool["mainEntity"] is grep
     inputs = workflow["input"]
     outputs = workflow["output"]
     assert len(inputs) == 2