--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_phylogeny.xml	Thu May 18 09:34:15 2017 -0400
@@ -0,0 +1,136 @@
+<tool id="qiime_make_phylogeny" name="Make phylogeny" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="8.2.9">raxml</requirement>
+        <requirement type="package" version="2.1">clustalw</requirement>
+        <requirement type="package" version="3.8.1551">muscle</requirement>
+        <requirement type="package" version="1.0.9">clearcut</requirement>
+    </expand>
+    <version_command>make_phylogeny.py --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        make_phylogeny.py
+            --input_fp '$input_fp'
+            --result_fp '$result_fp'
+            --tree_method '$tree_method'
+            --log_fp '$log_fp'
+            --root_method '$root_method'
+    ]]></command>
+    <inputs>
+        <param argument="--input_fp" type="data" format="fasta" label="Input fasta alignment"/>
+        <param argument="--tree_method" type="select" label="Method for tree building">
+            <option value="clustalw">ClustalW</option>
+            <option value="raxml_v730">raxml_v730</option>
+            <option value="muscle">muscle</option>
+            <option value="fasttree" selected="true">fasttree</option>
+            <option value="clearcut">clearcut</option>
+        </param>
+        <param argument="--root_method" type="select" label="Method for choosing root of phylo tree">
+            <option value="midpoint">Midpoint</option>
+            <option value="tree_method_default" selected="true">Default method of tree method</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="result_fp" format="nhx" label="${tool.name} on ${on_string}: Tree"/>
+        <data name="log_fp" format="txt" label="${tool.name} on ${on_string}: Log"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
+            <param name="tree_method" value="fasttree"/>
+            <param name="root_method" value="tree_method_default" />
+            <output name="result_fp" file="make_phylogeny/fasttree_tree_method_default.tre"/>
+            <output name="log_fp">
+                <assert_contents>
+                    <has_text text="Method:fasttree"/>
+                    <has_text text="CogentTreeBuilder parameters:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
+            <param name="tree_method" value="raxml_v730"/>
+            <param name="root_method" value="tree_method_default" />
+            <output name="result_fp" ftype="nhx" >
+                <assert_contents>
+                    <has_text text="seq_20"/>
+                    <has_text text="seq_46"/>
+                    <has_text text="seq_11"/>
+                </assert_contents>
+            </output>
+	    <output name="log_fp">
+                <assert_contents>
+                    <has_text text="Method:raxml_v730"/>
+                    <has_text text="CogentTreeBuilder parameters:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
+            <param name="tree_method" value="muscle"/>
+            <param name="root_method" value="tree_method_default" />
+            <output name="result_fp" file="make_phylogeny/muscle.tre"/>
+            <output name="log_fp">
+                <assert_contents>
+                    <has_text text="Method:muscle"/>
+                    <has_text text="CogentTreeBuilder parameters:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
+            <param name="tree_method" value="clustalw"/>
+            <param name="root_method" value="tree_method_default" />
+            <output name="result_fp" file="make_phylogeny/clustalw.tre"/>
+            <output name="log_fp">
+                <assert_contents>
+                    <has_text text="Method:clustalw"/>
+                    <has_text text="CogentTreeBuilder parameters:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
+            <param name="tree_method" value="clearcut"/>
+            <param name="root_method" value="tree_method_default" />
+            <output name="result_fp" ftype="nhx" >
+                <assert_contents>
+                    <has_text text="seq_20"/>
+                    <has_text text="seq_46"/>
+                    <has_text text="seq_11"/>
+                </assert_contents>
+            </output>
+            <output name="log_fp">
+                <assert_contents>
+                    <has_text text="Method:clearcut"/>
+                    <has_text text="CogentTreeBuilder parameters:"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_fp" value="make_phylogeny/aligned.fasta"/>
+            <param name="tree_method" value="fasttree"/>
+            <param name="root_method" value="midpoint" />
+            <output name="result_fp" file="make_phylogeny/fasttree_midpoint.tre"/>
+            <output name="log_fp">
+                <assert_contents>
+                    <has_text text="Method:fasttree"/>
+                    <has_text text="CogentTreeBuilder parameters:"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool produces a tree from a multiple sequence alignment. Trees are constructed with a set of sequences representative of the OTUs
+
+More information about this tool is available on
+`QIIME documentation <http://qiime.org/scripts/make_phylogeny.html>`_.
+    ]]></help>
+    <citations>
+        <expand macro="citations"/>
+    </citations>
+</tool>