Mercurial > repos > bebatut > graphlan
changeset 0:83baf73b0e79 draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit 7aadbbdef6da644837f62ea428cb859eeff34f04-dirty
| author | bebatut |
|---|---|
| date | Thu, 26 May 2016 09:38:11 -0400 |
| parents | |
| children | |
| files | graphlan.xml graphlan_annotate.xml graphlan_macros.xml test-data/input_annotation.txt test-data/input_tree.txt test-data/intermediary_tree.txt test-data/png_image.png tool_dependencies.xml |
| diffstat | 8 files changed, 857 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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>
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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>