xrefs yaml parser

lib/galaxy/tool_util/parser/yaml.py

@@ -41,7 +41,14 @@ class YamlToolSource(ToolSource):
         return self.root_dict.get("edam_topics", [])
 
     def parse_xrefs(self):
-        return self.root_dict.get("xrefs", [])
+        xrefs = []
+        rval = dict(
+            xrefs=xrefs
+        )
+        for i, xref_dict in enumerate(self.root_dict.get("xrefs", [])):
+            if xref_dict["type"] == "bio.tools"
+                xrefs.append(xref_dict["value"])
+        return rval
 
     def parse_is_multi_byte(self):
         return self.root_dict.get("is_multi_byte", self.default_is_multi_byte)
@@ -173,7 +180,6 @@ class YamlToolSource(ToolSource):
             python_template_version = packaging.version.parse(python_template_version)
         return python_template_version
 
-
 def _parse_test(i, test_dict):
     inputs = test_dict["inputs"]
     if is_dict(inputs):

test/unit/tools/test_parsing.py

@@ -87,6 +87,9 @@ class: GalaxyTool
 id: bowtie
 version: 1.0.2
 description: "The Bowtie Mapper"
+xrefs:
+  - type: bio.tools
+    value: bwa
 command: "bowtie_wrapper.pl --map-the-stuff"
 interpreter: "perl"
 runtime_version: