--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dram_set_database_locations.xml	Thu Sep 01 17:16:35 2022 +0000
@@ -0,0 +1,52 @@
+<tool id="dram_set_database_locations" name="DRAM: set database locations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>after installation by the data manager</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/dram_set_database_locations.py'
+$skip_uniref
+--db_version '$db_version'
+--galaxy_data_manager_data_path '$galaxy_data_manager_data_path'
+--output '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--skip_uniref" type="boolean" truevalue="--skip_uniref" falsevalue="" checked="false" label="Did you skip downloading and processing uniref when you installed the DRAM databases?"/>
+        <param name="db_version" type="text" value="1.3.5" label="DRAM database version">
+            <expand macro="sanitizer"/>
+        </param>
+        <param name="galaxy_data_manager_data_path" type="text" value="" label="Absolute Galaxy data manager data path" help="This is the absolute path for the Galaxy tool-data config setting">
+            <expand macro="sanitizer"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+    </outputs>
+    <tests>
+        <test expect_failure="true">
+            <param name="skip_uniref" value="true"/>
+            <param name="galaxy_data_manager_data_path" value="/gx/tool-data"/>
+            <assert_stderr>
+                <has_text text="error: unrecognized arguments: db: None"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
+Use of this tool should be restricted to a Galaxy administrator.  This tool updates the DRAM configuration file
+with the location of the databases after installation by the data manager.  This is necessary because DRAM creates
+a configuration file during installation, but the file is written before the Galaxy job finishes, so the database
+locations are relative to the job working directory instead of the configured GALAXY_DATA_MANAGER_DATA_PATH.
+
+It may be more ideal to perform this task as a second step in the data manager tool, but DRAM will not allow
+the configuration file to be updated to point to locations unless the databases exist in those locations.  But
+the data manager tool moves the databases to these locations as its last step, making it impossible to update
+the DRAM configuration file as a second step of that tool.
+
+See https://github.com/WrightonLabCSU/DRAM/wiki/5.-Managing%2C-updating-or-moving-a-DRAM-installation-and-databases for details.
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkaa621</citation>
+    </citations>
+</tool>
+