--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ete_species_tree_generator.xml	Fri Mar 17 16:23:39 2017 -0400
@@ -0,0 +1,90 @@
+<tool id="ete_species_tree_generator" name="ETE species tree generator" version="3.0.0b35">
+    <description>from a list of species using the ETE Toolkit</description>
+     <requirements>
+        <requirement type="package" version="3.0.0b35">ete3</requirement>
+    </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+    <![CDATA[
+python $__tool_directory__/ete_species_tree_generator.py
+-s '$speciesFile'
+#if $output_format.treebest == 'yes'
+    -f 8
+#else
+    -f ${output_format.format_selector}
+#end if
+-t $output_format.treebest
+-d $database
+    ]]>
+    </command>
+    <inputs>
+        <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />        
+        <conditional name="output_format">
+            <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes" />
+            <when value="no">
+                <param name="format_selector" type="select" label="Output format" help="See table below">
+                    <option value="0" selected="true">Flexible with support values (0)</option>
+                    <option value="1">Flexible with internal node names (1)</option>
+                    <option value="2">All branches + leaf names + internal supports (2)</option>
+                    <option value="3">All branches + all names (3)</option>
+                    <option value="4">Leaf branches + leaf names (4)</option>
+                    <option value="5">Internal and leaf branches + leaf names (5)</option>
+                    <option value="6">Internal branches + leaf names (6)</option>
+                    <option value="7">Leaf branches + all names (7)</option>
+                    <option value="8">All names (8)</option>
+                    <option value="9">Leaf names (9)</option>
+                    <option value="100">Topology only (100)</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="speciesFile" ftype="txt" value="species.txt" />
+            <param name="treebest" value="yes" />
+            <output name="outputFile" file="out.nhx" />
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+Generate a species tree from a list of species using the `ETE Toolkit`_.
+
+.. _ETE Toolkit: http://etetoolkit.org/
+
+**Output format:**
+
+======= ============================================= ========================================================================================
+FORMAT  DESCRIPTION                                     SAMPLE
+------- --------------------------------------------- ----------------------------------------------------------------------------------------
+0       flexible with support values                    ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
+1       flexible with internal node names               ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
+2       all branches + leaf names + internal supports   ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
+3       all branches + all names                        ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
+4       leaf branches + leaf names                      ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
+5       internal and leaf branches + leaf names         ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788);
+6       internal branches + leaf names                  ((D,F):0.067192,(B,H):0.807788);
+7       leaf branches + all names                       ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
+8       all names                                       ((D,F)E,(B,H)B);
+9       leaf names                                      ((D,F),(B,H));
+100     topology only                                   ((,),(,));
+======= ============================================= ========================================================================================
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/molbev/msw046</citation>
+    </citations>
+</tool>