# HG changeset patch
# User bebatut
# Date 1464269891 14400
# Node ID 83baf73b0e7920dcf3c55ba8271664579e2c1e8a

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty

diff -r 000000000000 -r 83baf73b0e79 graphlan.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphlan.xml	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,122 @@
+<tool id="graphlan" name="GraPhlAn" version="0.9.7">
+
+    <description>to produce graphical output of an input tree</description>
+
+    <macros>
+        <import>graphlan_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+
+    <stdio>
+        <regex match="Warning"
+               source="stderr"
+               level="warning"
+               description="" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+graphlan.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        graphlan.py
+            --format $format
+
+            #if $dpi
+                --dpi $dpi
+            #end if
+
+            --size $size
+
+            #if $pad
+                --pad $pad
+            #end if
+
+            $input_tree
+
+            #if str($format) == "png"
+                $png_output_image
+            #else if str($format) == "pdf"
+                $pdf_output_image
+            #else if str($format) == "ps"
+                $ps_output_image
+            #else if str($format) == "eps"
+                $eps_output_image
+            #else
+                $svg_output_image
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_tree" type="data" format="txt" label="Input tree" help="The tree must be in PhlyloXML, Newick or text format."/>
+
+        <param name='format' type="select" label="Output format" help="(--format)">
+            <option value="png" selected="true">PNG</option>
+            <option value="pdf">PDF</option>
+            <option value="ps">PS</option>
+            <option value="eps">EPS</option>
+            <option value="svg">SVG</option>
+        </param>
+
+        <param name="dpi" type="integer" label="Dpi of the output image
+            (Optional)" help="For non vectorial formats (--dpi)" optional="True"/>
+
+        <param name="size" type="integer" value="7" label="Size of the output image
+            (in inches)" help="(--size)"/>
+
+        <param name="pad" type="integer" label="Distance between the most external 
+            graphical element and the border of the image (Optional)" 
+            help="(--pad)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data format="png" name="png_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="png"</filter>
+        </data>
+        <data format="pdf" name="pdf_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="pdf"</filter>
+        </data>
+        <data format="ps" name="ps_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="ps"</filter>
+        </data>
+        <data format="eps" name="eps_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="eps"</filter>
+        </data>
+        <data format="svg" name="svg_output_image" 
+            label="${tool.name} on ${on_string}: Image">
+            <filter>format=="svg"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_tree" value="intermediary_tree.txt"/>
+            <param name="format" value="png"/>
+            <param name="dpi" value="100"/>
+            <param name="size" value="7"/>
+            <param name="pad" value="2"/>
+            <output name="png_output_image" file="png_image.png" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
+
+For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
diff -r 000000000000 -r 83baf73b0e79 graphlan_annotate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphlan_annotate.xml	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,70 @@
+<tool id="graphlan_annotate" name="Generation, personalization and annotation of tree" version="0.9.7">
+
+    <description>for GraPhlAn</description>
+
+    <macros>
+        <import>graphlan_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+
+    <stdio>
+        <regex match="Warning"
+               source="stderr"
+               level="warning"
+               description="" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+graphlan_annotate.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        graphlan_annotate.py
+            #if $annot
+                --annot $annot
+            #end if
+
+            $input_tree
+            $output_tree
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_tree" type="data" format="txt" label="Input tree" help="Newick, Nexus, PhyloXML or plain text"/>
+
+        <param name="annot" type="data" format="txt" label="Annotation file (Optional)" help="The annotation file is a tab-delimited file listing the graphical options for clades(--annot)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output_tree" 
+            label="${tool.name} on ${on_string}: Tree in PhyloXML" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_tree" value="input_tree.txt" />
+            <param name="annot" value="input_annotation.txt" />
+            <output name="output_tree" file="intermediary_tree.txt" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
+
+`graphlan_annotate` modifies any input tree (in any of the three standard format) adding additional information regarding structural or graphical aspects of the tree (like colors and style of the taxa, labels, shadows, heatmaps, ...).
+
+The annotation file is a tab-delimited file listing the graphical options for clades. Usually each line has three fields: the name of the clade, the name of the option, and the value to assign to the option. Lines can however have two fields (typically for "global" option not referred to a specific clade) or four fields when the external rings (a sort of circular heatmap) is specified.
+
+For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 83baf73b0e79 graphlan_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphlan_macros.xml	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,10 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.66">biopython</requirement>
+            <requirement type="package" version="1.4">matplotlib</requirement>
+            <requirement type="package" version="1.0.0">graphlan</requirement>
+        </requirements>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r 83baf73b0e79 test-data/input_annotation.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_annotation.txt	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,107 @@
+clade_separation	0.5
+branch_bracket_depth	0.8
+branch_bracket_width	0.2
+annotation_legend_font_size	10
+class_legend_font_size	10
+class_legend_marker_size	1.5
+
+FIRMICUTES	annotation	FIRMICUTES
+FIRMICUTES	clade_marker_color	#2d19ff
+FIRMICUTES	clade_marker_size	40
+
+PROTEOBACTERIA	annotation	PROTEOBACTERIA
+PROTEOBACTERIA	clade_marker_color	#29cc36
+PROTEOBACTERIA	clade_marker_size	40
+
+k__Archaea	clade_marker_size	58.0748302504
+p__Euryarchaeota	clade_marker_size	58.0748302504
+c__Methanobacteria	clade_marker_size	58.0748302504
+o__Methanobacteriales	clade_marker_size	58.0748302504
+f__Methanobacteriaceae	clade_marker_size	58.0748302504
+g__Methanobrevibacter	clade_marker_size	58.0748302504
+s__Methanobrevibacter_smithii	clade_marker_size	58.0748302504
+t__Methanobrevibacter_smithii_unclassified	clade_marker_size	58.0748302504
+k__Bacteria	clade_marker_size	200.0
+p__Actinobacteria	clade_marker_size	22.66961905
+c__Actinobacteria	clade_marker_size	22.66961905
+o__Actinomycetales	clade_marker_size	22.66961905
+f__Propionibacteriaceae	clade_marker_size	22.66961905
+g__Propionibacterium	clade_marker_size	22.66961905
+s__Propionibacterium_acnes	clade_marker_size	22.66961905
+t__Propionibacterium_acnes_unclassified	clade_marker_size	22.66961905
+p__Deinococcus_Thermus	clade_marker_size	22.298886707
+c__Deinococci	clade_marker_size	22.298886707
+o__Deinococcales	clade_marker_size	22.298886707
+f__Deinococcaceae	clade_marker_size	22.298886707
+g__Deinococcus	clade_marker_size	22.298886707
+s__Deinococcus_radiodurans	clade_marker_size	21.1340492974
+t__GCF_000008565	clade_marker_size	21.1340492974
+s__Deinococcus_unclassified	clade_marker_size	21.1817307606
+p__Firmicutes	clade_marker_size	183.285013514
+p__Firmicutes	clade_marker_color	#2d19ff
+c__Bacilli	clade_marker_size	182.398015269
+c__Bacilli	clade_marker_color	#2d19ff
+o__Bacillales	clade_marker_size	164.332515943
+o__Bacillales	clade_marker_color	#2d19ff
+f__Staphylococcaceae	clade_marker_size	164.332515943
+f__Staphylococcaceae	clade_marker_color	#2d19ff
+g__Staphylococcus	clade_marker_size	164.332515943
+g__Staphylococcus	clade_marker_color	#2d19ff
+s__Staphylococcus_aureus	clade_marker_size	122.793996615
+s__Staphylococcus_aureus	clade_marker_color	#2d19ff
+t__Staphylococcus_aureus_unclassified	clade_marker_size	122.793996615
+t__Staphylococcus_aureus_unclassified	clade_marker_color	#2d19ff
+s__Staphylococcus_epidermidis	clade_marker_size	120.392106048
+s__Staphylococcus_epidermidis	clade_marker_color	#2d19ff
+t__Staphylococcus_epidermidis_unclassified	clade_marker_size	120.392106048
+t__Staphylococcus_epidermidis_unclassified	clade_marker_color	#2d19ff
+o__Lactobacillales	clade_marker_size	96.1062970373
+f__Streptococcaceae	clade_marker_size	96.1062970373
+g__Streptococcus	clade_marker_size	96.1062970373
+s__Streptococcus_agalactiae	clade_marker_size	25.9449465996
+t__Streptococcus_agalactiae_unclassified	clade_marker_size	25.9449465996
+s__Streptococcus_mutans	clade_marker_size	93.7375603
+t__Streptococcus_mutans_unclassified	clade_marker_size	93.7375603
+c__Clostridia	clade_marker_size	26.8159954288
+o__Clostridiales	clade_marker_size	26.8159954288
+f__Clostridiaceae	clade_marker_size	26.8159954288
+g__Clostridium	clade_marker_size	26.8159954288
+s__Clostridium_beijerinckii	clade_marker_size	26.8159954288
+t__Clostridium_beijerinckii_unclassified	clade_marker_size	26.8159954288
+p__Proteobacteria	clade_marker_size	102.159086265
+p__Proteobacteria	clade_marker_color	#29cc36
+c__Alphaproteobacteria	clade_marker_size	53.6955516997
+o__Rhodobacterales	clade_marker_size	53.6955516997
+f__Rhodobacteraceae	clade_marker_size	53.6955516997
+g__Rhodobacter	clade_marker_size	53.6955516997
+s__Rhodobacter_sphaeroides	clade_marker_size	53.6955516997
+t__Rhodobacter_sphaeroides_unclassified	clade_marker_size	53.6955516997
+c__Betaproteobacteria	clade_marker_size	20.3264778878
+o__Neisseriales	clade_marker_size	20.3264778878
+f__Neisseriaceae	clade_marker_size	20.3264778878
+g__Neisseria	clade_marker_size	20.3264778878
+s__Neisseria_meningitidis	clade_marker_size	20.3264778878
+t__Neisseria_meningitidis_unclassified	clade_marker_size	20.3264778878
+c__Epsilonproteobacteria	clade_marker_size	20.5761787104
+o__Campylobacterales	clade_marker_size	20.5761787104
+f__Helicobacteraceae	clade_marker_size	20.5761787104
+g__Helicobacter	clade_marker_size	20.5761787104
+s__Helicobacter_pylori	clade_marker_size	20.5761787104
+t__Helicobacter_pylori_unclassified	clade_marker_size	20.5761787104
+c__Gammaproteobacteria	clade_marker_size	85.4517057547
+o__Enterobacteriales	clade_marker_size	78.466031643
+f__Enterobacteriaceae	clade_marker_size	78.466031643
+g__Escherichia	clade_marker_size	78.466031643
+s__Escherichia_coli	clade_marker_size	58.9341374431
+t__Escherichia_coli_unclassified	clade_marker_size	58.9341374431
+s__Escherichia_unclassified	clade_marker_size	49.960616022
+o__Pseudomonadales	clade_marker_size	34.0879564025
+f__Moraxellaceae	clade_marker_size	20.9013800671
+g__Acinetobacter	clade_marker_size	20.9013800671
+s__Acinetobacter_baumannii	clade_marker_size	20.9013800671
+t__Acinetobacter_baumannii_unclassified	clade_marker_size	20.9013800671
+f__Pseudomonadaceae	clade_marker_size	33.3271759768
+g__Pseudomonas	clade_marker_size	33.3271759768
+s__Pseudomonas_aeruginosa	clade_marker_size	25.8720239085
+t__Pseudomonas_aeruginosa_unclassified	clade_marker_size	25.8720239085
+s__Pseudomonas_unclassified	clade_marker_size	28.0078913105
diff -r 000000000000 -r 83baf73b0e79 test-data/input_tree.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_tree.txt	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,82 @@
+k__Archaea
+k__Archaea.p__Euryarchaeota
+k__Archaea.p__Euryarchaeota.c__Methanobacteria
+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales
+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae
+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter
+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter.s__Methanobrevibacter_smithii
+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter.s__Methanobrevibacter_smithii.t__Methanobrevibacter_smithii_unclassified
+k__Bacteria
+k__Bacteria.p__Actinobacteria
+k__Bacteria.p__Actinobacteria.c__Actinobacteria
+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales
+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae
+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium
+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium.s__Propionibacterium_acnes
+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium.s__Propionibacterium_acnes.t__Propionibacterium_acnes_unclassified
+k__Bacteria.p__Deinococcus_Thermus
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_radiodurans
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_radiodurans.t__GCF_000008565
+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_unclassified
+k__Bacteria.p__Firmicutes
+k__Bacteria.p__Firmicutes.c__Bacilli
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_aureus
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_aureus.t__Staphylococcus_aureus_unclassified
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_epidermidis
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_epidermidis.t__Staphylococcus_epidermidis_unclassified
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_agalactiae
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_agalactiae.t__Streptococcus_agalactiae_unclassified
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_mutans
+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_mutans.t__Streptococcus_mutans_unclassified
+k__Bacteria.p__Firmicutes.c__Clostridia
+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales
+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae
+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae.g__Clostridium
+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae.g__Clostridium.s__Clostridium_beijerinckii
+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae.g__Clostridium.s__Clostridium_beijerinckii.t__Clostridium_beijerinckii_unclassified
+k__Bacteria.p__Proteobacteria
+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria
+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales
+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae
+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter
+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter.s__Rhodobacter_sphaeroides
+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter.s__Rhodobacter_sphaeroides.t__Rhodobacter_sphaeroides_unclassified
+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria
+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales
+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae
+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria
+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria.s__Neisseria_meningitidis
+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria.s__Neisseria_meningitidis.t__Neisseria_meningitidis_unclassified
+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria
+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales
+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae
+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter
+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter.s__Helicobacter_pylori
+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter.s__Helicobacter_pylori.t__Helicobacter_pylori_unclassified
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_coli
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_coli.t__Escherichia_coli_unclassified
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_unclassified
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter.s__Acinetobacter_baumannii
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter.s__Acinetobacter_baumannii.t__Acinetobacter_baumannii_unclassified
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_aeruginosa
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_aeruginosa.t__Pseudomonas_aeruginosa_unclassified
+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_unclassified
\ No newline at end of file
diff -r 000000000000 -r 83baf73b0e79 test-data/intermediary_tree.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intermediary_tree.txt	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,439 @@
+<phyloxml xmlns="http://www.phyloxml.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">
+  <phylogeny rooted="true">
+    <clade>
+      <clade>
+        <name>k__Archaea</name>
+        <branch_length>1.0</branch_length>
+        <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+        <clade>
+          <name>p__Euryarchaeota</name>
+          <branch_length>1.0</branch_length>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+          <clade>
+            <name>c__Methanobacteria</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+            <clade>
+              <name>o__Methanobacteriales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+              <clade>
+                <name>f__Methanobacteriaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+                <clade>
+                  <name>g__Methanobrevibacter</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+                  <clade>
+                    <name>s__Methanobrevibacter_smithii</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+                    <clade>
+                      <name>t__Methanobrevibacter_smithii_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.0748302504</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+        </clade>
+      </clade>
+      <clade>
+        <name>k__Bacteria</name>
+        <branch_length>1.0</branch_length>
+        <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">200.0</property>
+        <clade>
+          <name>p__Deinococcus_Thermus</name>
+          <branch_length>1.0</branch_length>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
+          <clade>
+            <name>c__Deinococci</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
+            <clade>
+              <name>o__Deinococcales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
+              <clade>
+                <name>f__Deinococcaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
+                <clade>
+                  <name>g__Deinococcus</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.298886707</property>
+                  <clade>
+                    <name>s__Deinococcus_unclassified</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1817307606</property>
+                  </clade>
+                  <clade>
+                    <name>s__Deinococcus_radiodurans</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1340492974</property>
+                    <clade>
+                      <name>t__GCF_000008565</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1340492974</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+        </clade>
+        <clade>
+          <name>p__Firmicutes</name>
+          <branch_length>1.0</branch_length>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">183.285013514</property>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+          <clade>
+            <name>c__Clostridia</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
+            <clade>
+              <name>o__Clostridiales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
+              <clade>
+                <name>f__Clostridiaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
+                <clade>
+                  <name>g__Clostridium</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
+                  <clade>
+                    <name>s__Clostridium_beijerinckii</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
+                    <clade>
+                      <name>t__Clostridium_beijerinckii_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+          <clade>
+            <name>c__Bacilli</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">182.398015269</property>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+            <clade>
+              <name>o__Bacillales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">164.332515943</property>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+              <clade>
+                <name>f__Staphylococcaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">164.332515943</property>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+                <clade>
+                  <name>g__Staphylococcus</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">164.332515943</property>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+                  <clade>
+                    <name>s__Staphylococcus_aureus</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">122.793996615</property>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+                    <clade>
+                      <name>t__Staphylococcus_aureus_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">122.793996615</property>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+                    </clade>
+                  </clade>
+                  <clade>
+                    <name>s__Staphylococcus_epidermidis</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">120.392106048</property>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+                    <clade>
+                      <name>t__Staphylococcus_epidermidis_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">120.392106048</property>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#2d19ff</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+            <clade>
+              <name>o__Lactobacillales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">96.1062970373</property>
+              <clade>
+                <name>f__Streptococcaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">96.1062970373</property>
+                <clade>
+                  <name>g__Streptococcus</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">96.1062970373</property>
+                  <clade>
+                    <name>s__Streptococcus_mutans</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">93.7375603</property>
+                    <clade>
+                      <name>t__Streptococcus_mutans_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">93.7375603</property>
+                    </clade>
+                  </clade>
+                  <clade>
+                    <name>s__Streptococcus_agalactiae</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.9449465996</property>
+                    <clade>
+                      <name>t__Streptococcus_agalactiae_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.9449465996</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+        </clade>
+        <clade>
+          <name>p__Actinobacteria</name>
+          <branch_length>1.0</branch_length>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+          <clade>
+            <name>c__Actinobacteria</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+            <clade>
+              <name>o__Actinomycetales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+              <clade>
+                <name>f__Propionibacteriaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+                <clade>
+                  <name>g__Propionibacterium</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+                  <clade>
+                    <name>s__Propionibacterium_acnes</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+                    <clade>
+                      <name>t__Propionibacterium_acnes_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">22.66961905</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+        </clade>
+        <clade>
+          <name>p__Proteobacteria</name>
+          <branch_length>1.0</branch_length>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">102.159086265</property>
+          <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_color" ref="A:1">#29cc36</property>
+          <clade>
+            <name>c__Gammaproteobacteria</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">85.4517057547</property>
+            <clade>
+              <name>o__Enterobacteriales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">78.466031643</property>
+              <clade>
+                <name>f__Enterobacteriaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">78.466031643</property>
+                <clade>
+                  <name>g__Escherichia</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">78.466031643</property>
+                  <clade>
+                    <name>s__Escherichia_coli</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.9341374431</property>
+                    <clade>
+                      <name>t__Escherichia_coli_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">58.9341374431</property>
+                    </clade>
+                  </clade>
+                  <clade>
+                    <name>s__Escherichia_unclassified</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">49.960616022</property>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+            <clade>
+              <name>o__Pseudomonadales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">34.0879564025</property>
+              <clade>
+                <name>f__Moraxellaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
+                <clade>
+                  <name>g__Acinetobacter</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
+                  <clade>
+                    <name>s__Acinetobacter_baumannii</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
+                    <clade>
+                      <name>t__Acinetobacter_baumannii_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.9013800671</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+              <clade>
+                <name>f__Pseudomonadaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">33.3271759768</property>
+                <clade>
+                  <name>g__Pseudomonas</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">33.3271759768</property>
+                  <clade>
+                    <name>s__Pseudomonas_unclassified</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">28.0078913105</property>
+                  </clade>
+                  <clade>
+                    <name>s__Pseudomonas_aeruginosa</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.8720239085</property>
+                    <clade>
+                      <name>t__Pseudomonas_aeruginosa_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.8720239085</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+          <clade>
+            <name>c__Alphaproteobacteria</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
+            <clade>
+              <name>o__Rhodobacterales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
+              <clade>
+                <name>f__Rhodobacteraceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
+                <clade>
+                  <name>g__Rhodobacter</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
+                  <clade>
+                    <name>s__Rhodobacter_sphaeroides</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
+                    <clade>
+                      <name>t__Rhodobacter_sphaeroides_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">53.6955516997</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+          <clade>
+            <name>c__Betaproteobacteria</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
+            <clade>
+              <name>o__Neisseriales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
+              <clade>
+                <name>f__Neisseriaceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
+                <clade>
+                  <name>g__Neisseria</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
+                  <clade>
+                    <name>s__Neisseria_meningitidis</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
+                    <clade>
+                      <name>t__Neisseria_meningitidis_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.3264778878</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+          <clade>
+            <name>c__Epsilonproteobacteria</name>
+            <branch_length>1.0</branch_length>
+            <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
+            <clade>
+              <name>o__Campylobacterales</name>
+              <branch_length>1.0</branch_length>
+              <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
+              <clade>
+                <name>f__Helicobacteraceae</name>
+                <branch_length>1.0</branch_length>
+                <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
+                <clade>
+                  <name>g__Helicobacter</name>
+                  <branch_length>1.0</branch_length>
+                  <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
+                  <clade>
+                    <name>s__Helicobacter_pylori</name>
+                    <branch_length>1.0</branch_length>
+                    <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
+                    <clade>
+                      <name>t__Helicobacter_pylori_unclassified</name>
+                      <branch_length>1.0</branch_length>
+                      <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">20.5761787104</property>
+                    </clade>
+                  </clade>
+                </clade>
+              </clade>
+            </clade>
+          </clade>
+        </clade>
+      </clade>
+    </clade>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="class_legend_marker_size" ref="A:1">1.5</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="class_legend_font_size" ref="A:1">10</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="branch_bracket_depth" ref="A:1">0.8</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="clade_separation" ref="A:1">0.5</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="branch_bracket_width" ref="A:1">0.2</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="annotation_legend_font_size" ref="A:1">10</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_keys" ref="A:1">FIRMICUTES_._._PROTEOBACTERIA</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_annotation_background_color" ref="A:1">._._._.</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_annotation_background_edge_color" ref="A:1">._._._.</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_color" ref="A:1">#2d19ff_._._#29cc36</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_edge_width" ref="A:1">._._._.</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="leg_clade_marker_size" ref="A:1">40_._._40</property>
+    <property applies_to="phylogeny" datatype="xsd:string" id_ref="ignore_branch_len" ref="A:1">1</property>
+  </phylogeny>
+</phyloxml>
\ No newline at end of file
diff -r 000000000000 -r 83baf73b0e79 test-data/png_image.png
Binary file test-data/png_image.png has changed
diff -r 000000000000 -r 83baf73b0e79 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 26 09:38:11 2016 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="biopython" version="1.66">
+        <repository changeset_revision="8433ee4531ff" name="package_biopython_1_66" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository changeset_revision="f7424e1cf115" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="graphlan" version="1.0.0">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">
+                    hg clone -u 1.0 https://hg@bitbucket.org/nsegata/graphlan
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin/</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="GRAPHLAN_DIR">$INSTALL_DIR/</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme />
+    </package>
+</tool_dependency>