--- a/ete_species_tree_generator.xml	Fri Mar 17 16:23:39 2017 -0400
+++ b/ete_species_tree_generator.xml	Tue Nov 07 11:45:13 2017 -0500
@@ -1,27 +1,30 @@
-<tool id="ete_species_tree_generator" name="ETE species tree generator" version="3.0.0b35">
+<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@.1">
     <description>from a list of species using the ETE Toolkit</description>
-     <requirements>
-        <requirement type="package" version="3.0.0b35">ete3</requirement>
-    </requirements>
+    <macros>
+        <import>ete_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
     </stdio>
     <command>
     <![CDATA[
-python $__tool_directory__/ete_species_tree_generator.py
+python '$__tool_directory__/ete_species_tree_generator.py'
 -s '$speciesFile'
+-d $database
+-o '$outputFile'
 #if $output_format.treebest == 'yes'
     -f 8
 #else
     -f ${output_format.format_selector}
 #end if
 -t $output_format.treebest
--d $database
     ]]>
     </command>
     <inputs>
-        <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />        
+        <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
+        <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
         <conditional name="output_format">
             <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
                 <option value="yes">Yes</option>
@@ -44,19 +47,21 @@
                 </param>
             </when>
         </conditional>
-        <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)">
-            <option value="no" selected="true">No</option>
-            <option value="yes">Yes</option>
-        </param>
     </inputs>
     <outputs>
-        <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/>
+        <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}"/>
     </outputs>
     <tests>
         <test>
             <param name="speciesFile" ftype="txt" value="species.txt" />
+            <param name="database" ftype="sqlite" value="taxdump.sqlite" />
             <param name="treebest" value="yes" />
-            <output name="outputFile" file="out.nhx" />
+            <output name="outputFile">
+                <assert_contents>
+                    <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" />
+                    <has_text text=")root;" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>
@@ -84,7 +89,5 @@
 ======= ============================================= ========================================================================================
     ]]>
     </help>
-    <citations>
-        <citation type="doi">10.1093/molbev/msw046</citation>
-    </citations>
+    <expand macro="citations" />
 </tool>