Fix remote shed tool config paths

Author: jmchilton

planemo/galaxy/config.py

@@ -63,7 +63,10 @@
     write_file,
 )
 from planemo.mulled import build_involucro_context
-from planemo.runnable import RunnableType
+from planemo.runnable import (
+    GALAXY_TOOLS_PREFIX,
+    RunnableType,
+)
 from planemo.shed import tool_shed_url
 from .api import (
     DEFAULT_ADMIN_API_KEY,
@@ -616,7 +619,12 @@ def _all_tool_paths(
 ) -> Set[str]:
     extra_tools = extra_tools or []
     all_tool_paths = {
-        r.path for r in runnables if r.has_tools and not r.data_manager_conf_path and not r.is_remote_workflow_uri
+        r.path
+        for r in runnables
+        if r.has_tools
+        and not r.data_manager_conf_path
+        and not r.is_remote_workflow_uri
+        and not r.uri.startswith(GALAXY_TOOLS_PREFIX)
     }
     extra_tools = _expand_paths(galaxy_root, extra_tools=extra_tools)
     all_tool_paths.update(extra_tools)

tests/test_galaxy_config.py

@@ -7,10 +7,15 @@
 import yaml
 
 from planemo.galaxy.config import (
+    _all_tool_paths,
     galaxy_config,
     get_refgenie_config,
     write_galaxy_config,
 )
+from planemo.runnable import (
+    for_path,
+    for_uri,
+)
 from .test_utils import (
     create_test_context,
     skip_if_environ,
@@ -58,6 +63,16 @@ def test_refgenie_config_version():
     assert yaml.load(refgenie_config, Loader=yaml.SafeLoader)["config_version"] == 0.3
 
 
+def test_all_tool_paths_excludes_remote_galaxy_tools():
+    local_tool = os.path.join(os.path.dirname(__file__), "data", "tools", "two_tests.xml")
+    remote_tool_id = "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.3"
+
+    tool_paths = _all_tool_paths([for_path(local_tool), for_uri(f"gxid://tools/{remote_tool_id}")])
+
+    assert local_tool in tool_paths
+    assert f"gxid://tools/{remote_tool_id}" not in tool_paths
+
+
 def _assert_property_is(config, prop, value):
     env_var = "GALAXY_CONFIG_OVERRIDE_%s" % prop.upper()
     assert config.env[env_var] == value