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Changeset 0:b344522045f3 (2016-04-20)

Next changeset 1:d7cf3b50a074 (2016-06-21)

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

added:
export2graphlan.xml
test-data/annotation_output.txt
test-data/input_profile.tabular
test-data/tree_output.txt
tool_dependencies.xml

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

[

b'@@ -0,0 +1,215 @@\n+<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">\n+\n+ <description></description>\n+\n+ <requirements>\n+ <requirement type="package" version="0.16">pandas</requirement>\n+ <requirement type="package" version="0.16">scipy</requirement>\n+ <requirement type="package" version="1.4">matplotlib</requirement>\n+ <requirement type="package" version="0.19">export2graphlan</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ </stdio>\n+\n+ <version_command>\n+<![CDATA[\n+export2graphlan.py -v\n+]]>\n+ </version_command>\n+\n+ <command>\n+<![CDATA[ \n+ export2graphlan.py\n+ -i $lefse_input\n+\n+ #if $lefse_output\n+ -o lefse_output\n+ #end if\n+\n+ -t $tree\n+ -a $annotation\n+\n+ #if $annotations\n+ --annotations $annotations\n+ #end if\n+\n+ #if $external_annotations\n+ --external_annotations $external_annotations\n+ #end if\n+\n+ #if $background_levels\n+ --background_levels $background_levels\n+ #end if\n+\n+ #if $background_clades\n+ --background_clades "$background_clades"\n+ #end if\n+\n+ #if $background_colors\n+ --background_colors "$background_colors"\n+ #end if\n+ \n+ #if $title\n+ --title "title"\n+ #end if\n+ \n+ --title_font_size $title_font_size \n+ --def_clade_size $def_clade_size \n+ --min_clade_size $min_clade_size\n+ --max_clade_size $max_clade_size\n+ --def_font_size $def_font_size\n+ --min_font_size $min_font_size\n+ --max_font_size $max_font_size\n+ --annotation_legend_font_size $annotation_legend_font_size\n+ --abundance_threshold $abundance_threshold\n+\n+ #if $most_abundant\n+ --most_abundant $most_abundant\n+ #end if\n+\n+ #if $least_biomarkers\n+ --least_biomarkers $least_biomarkers\n+ #end if\n+\n+ --fname_row $fname_row\n+ --sname_row $sname_row\n+\n+ #if $metadata_rows\n+ --metadata_rows $metadata_rows\n+ #end if\n+ \n+ #if $skip_rows \n+ --skip_rows $skip_rows\n+ #end if\n+\n+ #if $sperc\n+ --sperc $sperc\n+ #end if\n+\n+ #if $fperc\n+ --fperc $fperc\n+ #end if\n+\n+ #if $stop\n+ --stop $stop\n+ #end if\n+\n+ #if $ftop\n+ --ftop $ftop\n+ #end if\n+]]>\n+ </command>\n+\n+ <inputs>\n+ <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>\n+\n+ <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>\n+\n+ <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"/>\n+\n+ <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"/>\n+\n+ <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"/>\n+\n+ <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"/>\n+\n+ '..b'omarkers 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"/>\n+\n+ <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)"/>\n+\n+ <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)"/>\n+\n+ <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>\n+\n+ <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"/>\n+\n+ <param name="sperc" type="float" label="Percentile of sample value \n+ distribution for sample selection (Optional)" help="(--sperc)" \n+ optional="True"/>\n+\n+ <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>\n+\n+ <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"/>\n+\n+ <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"/>\n+ </inputs>\n+\n+ <outputs>\n+ <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />\n+ <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="lefse_input" value="input_profile.tabular"/>\n+ <param name="annotations" value=""/>\n+ <param name="external_annotations" value=""/>\n+ <param name="background_levels" value=""/>\n+ <param name="background_clades" value=""/>\n+ <param name="background_colors" value=""/>\n+ <param name="title" value=""/>\n+ <param name="title_font_size" value="15"/>\n+ <param name="def_clade_size" value="10"/>\n+ <param name="min_clade_size" value="20"/>\n+ <param name="max_clade_size" value="200"/>\n+ <param name="def_font_size" value="10"/>\n+ <param name="min_font_size" value="8"/>\n+ <param name="max_font_size" value="12"/>\n+ <param name="annotation_legend_font_size" value="10"/>\n+ <param name="abundance_threshold" value="20.0"/>\n+ <param name="most_abundant" value=""/>\n+ <param name="least_biomarkers" value=""/>\n+ <param name="fname_row" value="0"/>\n+ <param name="sname_row" value="0" />\n+ <param name="metadata_rows" value=""/>\n+ <param name="skip_rows" value=""/>\n+ <param name="sperc" value=""/>\n+ <param name="fperc" value=""/>\n+ <param name="stop" value=""/>\n+ <param name="ftop" value=""/>\n+ <output name="annotation" file="annotation_output.txt"/>\n+ <output name="tree" file="tree_output.txt"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+\n+**What it does**\n+\n+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\n+\n+In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. \n+\n+For more information, check the \n+`user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.\n+\n+ ]]></help>\n+\n+ <citations>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n'

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

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

b'@@ -0,0 +1,82 @@\n+k__Archaea\n+k__Archaea.p__Euryarchaeota\n+k__Archaea.p__Euryarchaeota.c__Methanobacteria\n+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales\n+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae\n+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter\n+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter.s__Methanobrevibacter_smithii\n+k__Archaea.p__Euryarchaeota.c__Methanobacteria.o__Methanobacteriales.f__Methanobacteriaceae.g__Methanobrevibacter.s__Methanobrevibacter_smithii.t__Methanobrevibacter_smithii_unclassified\n+k__Bacteria\n+k__Bacteria.p__Actinobacteria\n+k__Bacteria.p__Actinobacteria.c__Actinobacteria\n+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales\n+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae\n+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium\n+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium.s__Propionibacterium_acnes\n+k__Bacteria.p__Actinobacteria.c__Actinobacteria.o__Actinomycetales.f__Propionibacteriaceae.g__Propionibacterium.s__Propionibacterium_acnes.t__Propionibacterium_acnes_unclassified\n+k__Bacteria.p__Deinococcus_Thermus\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_radiodurans\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_radiodurans.t__GCF_000008565\n+k__Bacteria.p__Deinococcus_Thermus.c__Deinococci.o__Deinococcales.f__Deinococcaceae.g__Deinococcus.s__Deinococcus_unclassified\n+k__Bacteria.p__Firmicutes\n+k__Bacteria.p__Firmicutes.c__Bacilli\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_aureus\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_aureus.t__Staphylococcus_aureus_unclassified\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_epidermidis\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Bacillales.f__Staphylococcaceae.g__Staphylococcus.s__Staphylococcus_epidermidis.t__Staphylococcus_epidermidis_unclassified\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_agalactiae\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_agalactiae.t__Streptococcus_agalactiae_unclassified\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_mutans\n+k__Bacteria.p__Firmicutes.c__Bacilli.o__Lactobacillales.f__Streptococcaceae.g__Streptococcus.s__Streptococcus_mutans.t__Streptococcus_mutans_unclassified\n+k__Bacteria.p__Firmicutes.c__Clostridia\n+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales\n+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__Clostridiaceae\n+k__Bacteria.p__Firmicutes.c__Clostridia.o__Clostridiales.f__C'..b'beijerinckii.t__Clostridium_beijerinckii_unclassified\n+k__Bacteria.p__Proteobacteria\n+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria\n+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales\n+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae\n+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter\n+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter.s__Rhodobacter_sphaeroides\n+k__Bacteria.p__Proteobacteria.c__Alphaproteobacteria.o__Rhodobacterales.f__Rhodobacteraceae.g__Rhodobacter.s__Rhodobacter_sphaeroides.t__Rhodobacter_sphaeroides_unclassified\n+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria\n+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales\n+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae\n+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria\n+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria.s__Neisseria_meningitidis\n+k__Bacteria.p__Proteobacteria.c__Betaproteobacteria.o__Neisseriales.f__Neisseriaceae.g__Neisseria.s__Neisseria_meningitidis.t__Neisseria_meningitidis_unclassified\n+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria\n+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales\n+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae\n+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter\n+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter.s__Helicobacter_pylori\n+k__Bacteria.p__Proteobacteria.c__Epsilonproteobacteria.o__Campylobacterales.f__Helicobacteraceae.g__Helicobacter.s__Helicobacter_pylori.t__Helicobacter_pylori_unclassified\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_coli\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_coli.t__Escherichia_coli_unclassified\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Enterobacteriales.f__Enterobacteriaceae.g__Escherichia.s__Escherichia_unclassified\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter.s__Acinetobacter_baumannii\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Moraxellaceae.g__Acinetobacter.s__Acinetobacter_baumannii.t__Acinetobacter_baumannii_unclassified\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_aeruginosa\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_aeruginosa.t__Pseudomonas_aeruginosa_unclassified\n+k__Bacteria.p__Proteobacteria.c__Gammaproteobacteria.o__Pseudomonadales.f__Pseudomonadaceae.g__Pseudomonas.s__Pseudomonas_unclassified\n\\ No newline at end of file\n'

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>