Mercurial > repos > bebatut > graphlan
changeset 1:5cdaa98d9376 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit f20ebff87883fc5639f540418257ca04ce8296fb-dirty
| author | bebatut |
|---|---|
| date | Fri, 01 Apr 2016 05:51:57 -0400 |
| parents | c5746c07ca5e |
| children | 64e69b47b4ec |
| files | graphlan.xml graphlan_annotate.xml test-data/input_annotation.txt test-data/input_tree.txt test-data/output_image.png test-data/output_modified_tree.txt tool_dependencies.xml |
| diffstat | 7 files changed, 646 insertions(+), 9 deletions(-) [+] |
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--- a/graphlan.xml Mon Feb 01 07:45:14 2016 -0500 +++ b/graphlan.xml Fri Apr 01 05:51:57 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="graphlan" name="GraPhlAn" version="0.1.0"> +<tool id="graphlan" name="GraPhlAn" version="1.0"> <description>to produce graphical output of an input tree</description> @@ -13,13 +13,13 @@ <version_command> <![CDATA[ -python \${GRAPHLAN_DIR}/graphlan.py -v +graphlan.py -v ]]> </version_command> <command> <![CDATA[ - python \${GRAPHLAN_DIR}/graphlan.py + graphlan.py --format $format #if $dpi @@ -97,6 +97,12 @@ <tests> <test> + <param name="input_tree" value="output_modified_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" value="output_image.png" /> </test> </tests>
--- a/graphlan_annotate.xml Mon Feb 01 07:45:14 2016 -0500 +++ b/graphlan_annotate.xml Fri Apr 01 05:51:57 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="0.1.0"> +<tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="1.0"> <description></description> @@ -13,13 +13,13 @@ <version_command> <![CDATA[ -python \${GRAPHLAN_DIR}/graphlan_annotate.py -v +graphlan_annotate.py -v ]]> </version_command> <command> <![CDATA[ - python \${GRAPHLAN_DIR}/graphlan_annotate.py + graphlan_annotate.py #if $annot --annot $annot #end if @@ -38,12 +38,15 @@ </inputs> <outputs> - <data format="text" name="output_tree" + <data format="txt" name="output_tree" label="${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" value="output_modified_tree.txt" /> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_annotation.txt Fri Apr 01 05:51:57 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 Fri Apr 01 05:51:57 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/output_modified_tree.txt Fri Apr 01 05:51:57 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
--- a/tool_dependencies.xml Mon Feb 01 07:45:14 2016 -0500 +++ b/tool_dependencies.xml Fri Apr 01 05:51:57 2016 -0400 @@ -10,11 +10,11 @@ <install version="1.0"> <actions> <action type="shell_command"> - hg clone https://hg@bitbucket.org/nsegata/graphlan + 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/</destination_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>