Mercurial > repos > bebatut > export2graphlan
changeset 4:4a3676d020e7 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/export2graphlan/ commit 1b95965e1a861ec37867be554e324eb5bc1ece82-dirty
| author | bebatut |
|---|---|
| date | Wed, 20 Apr 2016 06:08:58 -0400 |
| parents | 953621231a6c |
| children | f05bc567f1a5 |
| files | export2graphlan.xml test-data/annotation_output.txt test-data/output_annotation.txt test-data/output_tree.txt test-data/tree_output.txt tool_dependencies.xml |
| diffstat | 6 files changed, 200 insertions(+), 196 deletions(-) [+] |
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--- a/export2graphlan.xml Fri Apr 01 05:51:29 2016 -0400 +++ b/export2graphlan.xml Wed Apr 20 06:08:58 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="export2graphlan" name="Export to GraPhlAn" version="0.1.0"> +<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19"> <description></description> @@ -6,7 +6,7 @@ <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="1.0">export2graphlan</requirement> + <requirement type="package" version="0.19">export2graphlan</requirement> </requirements> <stdio> @@ -192,8 +192,8 @@ <param name="fperc" value=""/> <param name="stop" value=""/> <param name="ftop" value=""/> - <output name="annotation" file="output_annotation.txt"/> - <output name="tree" file="output_tree.txt"/> + <output name="annotation" file="annotation_output.txt"/> + <output name="tree" file="tree_output.txt"/> </test> </tests> @@ -201,7 +201,11 @@ **What it does** -export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. 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 +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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation_output.txt Wed Apr 20 06:08:58 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
--- a/test-data/output_annotation.txt Fri Apr 01 05:51:29 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,107 +0,0 @@ -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
--- a/test-data/output_tree.txt Fri Apr 01 05:51:29 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,82 +0,0 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree_output.txt Wed Apr 20 06:08:58 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
--- a/tool_dependencies.xml Fri Apr 01 05:51:29 2016 -0400 +++ b/tool_dependencies.xml Wed Apr 20 06:08:58 2016 -0400 @@ -9,11 +9,11 @@ <package name="matplotlib" version="1.4"> <repository changeset_revision="9a4214646e88" name="package_python_2_7_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="export2graphlan" version="1.0"> + <package name="export2graphlan" version="0.19"> <install version="1.0"> <actions> <action type="shell_command"> - hg clone https://hg@bitbucket.org/CibioCM/export2graphlan + hg clone -r d6c10c1 https://hg@bitbucket.org/CibioCM/export2graphlan </action> <action type="move_file"> <source>export2graphlan.py</source>