--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/newick_display.xml	Mon Oct 01 09:46:08 2018 -0400
@@ -0,0 +1,137 @@
+<tool id="newick_display" name="Newick Display" version="1.6">
+    <description>visualize a phylogenetic tree</description>
+    <edam_operations>
+        <edam_operation>operation_0567</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="1.6">newick_utils</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+nw_display
+    #if $outformat != 'txt':
+        -s
+    #end if
+    $scalebar
+    -u '$legend'
+    -I 'r'
+    -i
+    #if $condbranchsupport.branchsupport == "true":
+        'fill:$condbranchsupport.supcolor;
+        font-size:$condbranchsupport.supfontsize;
+        transform:$condbranchsupport.suptransform;'
+    #else:
+        "visibility:hidden;"
+    #end if
+    -b
+    #if $condbranchlength.branchlength == "true":
+        'fill:$condbranchlength.lencolor;
+        font-size:$condbranchlength.lenfontsize;
+        transform:$condbranchlength.lentransform;'
+    #else:
+        "visibility:hidden;"
+    #end if
+
+    -l 'font-family:$leafFont;font-size:$leafSize;'
+    -d "stroke:grey;fill:none;stroke-width:2;stoke-linecap:round;"
+    -w  $width
+    $radial
+
+    '$fileNewick' > output.svg
+
+#if $outformat == 'png':
+    && convert output.svg output.png
+    && mv output.png '$output'
+#else:
+    && mv output.svg '$output'
+#end if
+
+    ]]></command>
+    <inputs>
+        <param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
+        <param name="scalebar" type="boolean" truevalue="" falsevalue="-S" checked="True" label="Display scale bar" />
+        <param name="legend" type="text" value="" label="Unit name for the scale bar" />
+        <param name="leafFont" type="text" value="sans-serif" label="Leaf font" />
+        <param name="leafSize" type="text" value="10px" label="Leaf font-size" />
+        <conditional name="condbranchsupport">
+            <param name="branchsupport" type="select" label="Branch support">
+                <option value="true">Display branch support</option>
+                <option value="false" selected="true">Hide branch support</option>
+            </param>
+            <when value="true">
+                <param name="supcolor" type="color" value="red" label="color" />
+                <param name="supfontsize" type="text" value="10px" label="font-size" />
+                <param name="suptransform" type="text" value="translateY(1.5em)" label="move" />
+            </when>
+            <when value="false" />
+        </conditional>
+        <conditional name="condbranchlength">
+            <param name="branchlength" type="select" label="Branch length">
+                <option value="true">Display branch length</option>
+                <option value="false" selected="true">Hide branch length</option>
+            </param>
+            <when value="true">
+                <param name="lencolor" type="color" value="blue" label="color" />
+                <param name="lenfontsize" type="text" value="10px" label="font-size" />
+                <param name="lentransform" type="text" value="translate(-1.5em,0em)" label="move" />
+            </when>
+            <when value="false" />
+        </conditional>
+        <param name="width" type="integer" value="800" label="Image width" help="in pixels for image output or in characters for text output" />
+        <param name="radial" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Draw a radial tree" />
+        <param name="outformat" type="select" label="Choose an output format">
+            <option value="svg" selected="true">SVG</option>
+            <option value="png">PNG</option>
+            <option value="txt">Text</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="svg" label="${tool.name} on ${on_string}: Tree Graph" >
+            <change_format>
+                <when input="outformat" value="png" format="png"/>
+                <when input="outformat" value="txt" format="txt"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fileNewick" value="tree.nwk"/>
+            <param name="width" value="400"/>
+            <param name="leafFont" value="courier"/>
+            <output name="output" file="tree.svg" ftype="svg" lines_diff="2"/>
+        </test>
+        <test><!-- test radial tree -->
+            <param name="fileNewick" value="tree.nwk"/>
+            <param name="radial" value="-r"/>
+            <param name="branchlength" value="true"/>
+            <output name="output" file="tree2.svg" ftype="svg" lines_diff="2"/>
+        </test>
+        <test><!-- test with png output format -->
+            <param name="fileNewick" value="tree.nwk"/>
+            <param name="radial" value="-r"/>
+            <param name="branchlength" value="true"/>
+            <param name="outformat" value="png"/>
+            <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
+        </test>
+         <test><!-- test with txt output format -->
+            <param name="fileNewick" value="tree.nwk"/>
+            <param name="outformat" value="txt"/>
+            <output name="output" file="tree.txt" ftype="txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool outputs a graph representing the tree, either as text or
+as a SVG or PNG image. Underscores in labels are replaced with spaces.
+Trees with no branch lengths are taken to be cladograms and are
+drawn with leaves aligned. Otherwise, the tree is assumed to be a
+phylogram: branch lengths are honored and a scale bar is drawn.
+
+.. image:: $PATH_TO_IMAGES/example.png
+   :alt: example newick tree graph
+
+   ]]></help>
+    <citations>
+        <citation type="doi">10.1186/1748-7188-3-7</citation>
+    </citations>
+</tool>