# HG changeset patch
# User bebatut
# Date 1461146969 14400
# Node ID b344522045f3efa11e94f35a14b3be0e502f9feb

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 1b95965e1a861ec37867be554e324eb5bc1ece82-dirty

diff -r 000000000000 -r b344522045f3 export2graphlan.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export2graphlan.xml	Wed Apr 20 06:09:29 2016 -0400
@@ -0,0 +1,215 @@
+<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">
+
+    <description></description>
+
+    <requirements>
+        <requirement type="package" version="0.16">pandas</requirement>
+        <requirement type="package" version="0.16">scipy</requirement>
+        <requirement type="package" version="1.4">matplotlib</requirement>
+        <requirement type="package" version="0.19">export2graphlan</requirement>
+    </requirements>
+
+    <stdio>
+    </stdio>
+
+    <version_command>
+<![CDATA[
+export2graphlan.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        export2graphlan.py
+            -i $lefse_input
+
+            #if $lefse_output
+                -o lefse_output
+            #end if
+
+            -t $tree
+            -a $annotation
+
+            #if $annotations
+                --annotations $annotations
+            #end if
+
+            #if $external_annotations
+                --external_annotations $external_annotations
+            #end if
+
+            #if $background_levels
+                --background_levels $background_levels
+            #end if
+
+            #if $background_clades
+                --background_clades "$background_clades"
+            #end if
+
+            #if $background_colors
+                --background_colors "$background_colors"
+            #end if
+ 
+            #if $title
+                --title "title"
+            #end if
+  
+            --title_font_size $title_font_size 
+            --def_clade_size $def_clade_size 
+            --min_clade_size $min_clade_size
+            --max_clade_size $max_clade_size
+            --def_font_size $def_font_size
+            --min_font_size $min_font_size
+            --max_font_size $max_font_size
+            --annotation_legend_font_size $annotation_legend_font_size
+            --abundance_threshold $abundance_threshold
+
+            #if $most_abundant
+                --most_abundant $most_abundant
+            #end if
+
+            #if $least_biomarkers
+                --least_biomarkers $least_biomarkers
+            #end if
+
+            --fname_row $fname_row
+            --sname_row $sname_row
+
+            #if $metadata_rows
+                --metadata_rows $metadata_rows
+            #end if
+                  
+            #if $skip_rows  
+                --skip_rows $skip_rows
+            #end if
+
+            #if $sperc
+                --sperc $sperc
+            #end if
+
+            #if $fperc
+                --fperc $fperc
+            #end if
+
+            #if $stop
+                --stop $stop
+            #end if
+
+            #if $ftop
+                --ftop $ftop
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
+
+        <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
+
+        <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/>
+
+        <param name="external_annotations" type="text" label="List which levels should use the external legend for the annotation (Optional)" help="The levels must be in comma-separated form (--external_annotations)" optional="True"/>
+
+        <param name="background_levels" type="text" label="List which levels should be highlight with a shaded background (Optional)" help="The levels must be in comma-separated form (--background_levels)" optional="True"/>
+
+        <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/>
+
+        <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)" optional="True"/>
+        
+        <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/>
+
+        <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/>
+
+        <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/>
+
+        <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/>
+
+        <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/>
+
+        <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/>
+
+        <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/>
+
+        <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/>
+
+        <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/>
+
+        <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/>
+
+        <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
+
+        <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/>
+
+        <param name="fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix (--fname_row)"/>
+
+        <param name="sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix (--sname_row)"/>
+
+        <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
+
+        <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/>
+
+        <param name="sperc" type="float" label="Percentile of sample value 
+            distribution for sample selection (Optional)" help="(--sperc)" 
+            optional="True"/>
+
+        <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>
+
+        <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/>
+
+        <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
+        <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="lefse_input" value="input_profile.tabular"/>
+            <param name="annotations" value=""/>
+            <param name="external_annotations" value=""/>
+            <param name="background_levels" value=""/>
+            <param name="background_clades" value=""/>
+            <param name="background_colors" value=""/>
+            <param name="title" value=""/>
+            <param name="title_font_size" value="15"/>
+            <param name="def_clade_size" value="10"/>
+            <param name="min_clade_size" value="20"/>
+            <param name="max_clade_size" value="200"/>
+            <param name="def_font_size" value="10"/>
+            <param name="min_font_size" value="8"/>
+            <param name="max_font_size" value="12"/>
+            <param name="annotation_legend_font_size" value="10"/>
+            <param name="abundance_threshold" value="20.0"/>
+            <param name="most_abundant" value=""/>
+            <param name="least_biomarkers" value=""/>
+            <param name="fname_row" value="0"/>
+            <param name="sname_row" value="0" />
+            <param name="metadata_rows" value=""/>
+            <param name="skip_rows" value=""/>
+            <param name="sperc" value=""/>
+            <param name="fperc" value=""/>
+            <param name="stop" value=""/>
+            <param name="ftop" value=""/>
+            <output name="annotation" file="annotation_output.txt"/>
+            <output name="tree" file="tree_output.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
+
+In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. 
+
+For more information, check the 
+`user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r b344522045f3 test-data/annotation_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation_output.txt	Wed Apr 20 06:09:29 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 b344522045f3 test-data/input_profile.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_profile.tabular	Wed Apr 20 06:09:29 2016 -0400
@@ -0,0 +1,83 @@
+#SampleID	Metaphlan2_Analysis
+k__Bacteria	93.482
+k__Archaea	6.518
+k__Bacteria|p__Firmicutes	73.48655
+k__Bacteria|p__Proteobacteria	19.32463
+k__Archaea|p__Euryarchaeota	6.518
+k__Bacteria|p__Actinobacteria	0.36084
+k__Bacteria|p__Deinococcus_Thermus	0.30999
+k__Bacteria|p__Firmicutes|c__Bacilli	72.54025
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	13.6073
+k__Archaea|p__Euryarchaeota|c__Methanobacteria	6.518
+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria	5.59702
+k__Bacteria|p__Firmicutes|c__Clostridia	0.9463
+k__Bacteria|p__Actinobacteria|c__Actinobacteria	0.36084
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci	0.30999
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria	0.07684
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria	0.04347
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales	55.42931
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	17.11093
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales	11.55615
+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales	6.518
+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales	5.59702
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales	2.05115
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales	0.9463
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales	0.36084
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales	0.30999
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales	0.07684
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales	0.04347
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae	55.42931
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae	17.11093
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae	11.55615
+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae	6.518
+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae	5.59702
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae	1.93069
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae	0.9463
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae	0.36084
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae	0.30999
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae	0.12046
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae	0.07684
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae	0.04347
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus	55.42931
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus	17.11093
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia	11.55615
+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter	6.518
+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter	5.59702
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas	1.93069
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium	0.9463
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium	0.36084
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus	0.30999
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter	0.12046
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter	0.07684
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria	0.04347
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_aureus	28.29995
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis	27.12936
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mutans	16.29021
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli	6.70485
+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii	6.518
+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter|s__Rhodobacter_sphaeroides	5.59702
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_unclassified	4.8513
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_unclassified	1.12042
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_beijerinckii	0.9463
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae	0.82072
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa	0.81027
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes	0.36084
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_unclassified	0.15821
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_radiodurans	0.15178
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii	0.12046
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter_pylori	0.07684
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria_meningitidis	0.04347
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_aureus|t__Staphylococcus_aureus_unclassified	28.29995
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis|t__Staphylococcus_epidermidis_unclassified	27.12936
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mutans|t__Streptococcus_mutans_unclassified	16.29021
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__Escherichia_coli_unclassified	6.70485
+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__Methanobrevibacter_smithii_unclassified	6.518
+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter|s__Rhodobacter_sphaeroides|t__Rhodobacter_sphaeroides_unclassified	5.59702
+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_beijerinckii|t__Clostridium_beijerinckii_unclassified	0.9463
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae|t__Streptococcus_agalactiae_unclassified	0.82072
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa|t__Pseudomonas_aeruginosa_unclassified	0.81027
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes|t__Propionibacterium_acnes_unclassified	0.36084
+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_radiodurans|t__GCF_000008565	0.15178
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii|t__Acinetobacter_baumannii_unclassified	0.12046
+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter_pylori|t__Helicobacter_pylori_unclassified	0.07684
+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria_meningitidis|t__Neisseria_meningitidis_unclassified	0.04347
diff -r 000000000000 -r b344522045f3 test-data/tree_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tree_output.txt	Wed Apr 20 06:09:29 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 b344522045f3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Apr 20 06:09:29 2016 -0400
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="pandas" version="0.16">
+        <repository changeset_revision="ea929a7f2976" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="scipy" version="0.16">
+        <repository changeset_revision="80f8536c6dc2" name="package_python_2_7_scipy_0_16" owner="iuc" 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="export2graphlan" version="0.19">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">
+                    hg clone -r d6c10c1 https://hg@bitbucket.org/CibioCM/export2graphlan
+                </action>
+                <action type="move_file">
+                    <source>export2graphlan.py</source>
+                    <destination>$INSTALL_DIR/bin/</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>hclust2</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin/hclust2/</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="EXPORT2GRAPHLAN_DIR">$INSTALL_DIR/</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme />
+    </package>
+</tool_dependency>