Fix transfer of $_TOOL_DIRECTORY subdirectories

Goes together with https://github.com/galaxyproject/pulsar/pull/385

lib/galaxy/dependencies/pinned-requirements.txt

@@ -133,7 +133,7 @@ prompt-toolkit==3.0.48
 propcache==0.2.0
 prov==1.5.1
 psutil==6.1.0
-pulsar-galaxy-lib==0.15.6
+pulsar-galaxy-lib==0.15.7
 pycparser==2.22
 pycryptodome==3.21.0
 pydantic==2.9.2

test/functional/tools/sample_tool_conf.xml

@@ -249,6 +249,7 @@
   <tool file="interactivetool_simple.xml" />
   <tool file="interactivetool_two_entry_points.xml" />
   <tool file="converter_target_datatype.xml" />
+  <tool file="tool_directory_copy.xml" />
 
   <!-- Tools interesting only for building up test workflows. -->
 

test/functional/tools/tool_directory_copy.xml

@@ -0,0 +1,16 @@
+<tool id="tool_directory_copy" name="tool_directory_copy" version="0.1.0" profile="24.2">
+    <!-- Copy a directory to a new location. -->
+    <command><![CDATA[
+cp -r '$__tool_directory__/realtime/simple' '$output_directory.extra_files_path'
+    ]]></command>
+    <outputs>
+        <data name="output_directory" format="directory" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output_directory" ftype="directory">
+                <extra_files type="file" name="Dockerfile" md5="ed0e3613e45ca9111121f78643afbb52"></extra_files>
+            </output>
+        </test>
+    </tests>
+</tool>

test/integration/test_pulsar_embedded.py

@@ -38,5 +38,6 @@ test_tools = integration_util.integration_tool_runner(
         "composite_output",
         "composite_output_tests",
         "detect_errors",
+        "tool_directory_copy",
     ]
 )