Mercurial > repos > bebatut > graphlan
changeset 2:64e69b47b4ec draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit fe1ede437f1b0e414d84d75e6a607047d1678444-dirty
| author | bebatut |
|---|---|
| date | Mon, 02 May 2016 05:44:20 -0400 |
| parents | 5cdaa98d9376 |
| children | dbb2478c7ee4 |
| files | graphlan.xml graphlan_annotate.xml graphlan_macros.xml test-data/intermediary_tree.txt test-data/output_image.png test-data/output_modified_tree.txt test-data/png_image.png tool_dependencies.xml |
| diffstat | 8 files changed, 485 insertions(+), 479 deletions(-) [+] |
line wrap: on
line diff
--- a/graphlan.xml Fri Apr 01 05:51:57 2016 -0400 +++ b/graphlan.xml Mon May 02 05:44:20 2016 -0400 @@ -1,14 +1,18 @@ -<tool id="graphlan" name="GraPhlAn" version="1.0"> +<tool id="graphlan" name="GraPhlAn" version="0.9.7"> <description>to produce graphical output of an input tree</description> - <requirements> - <requirement type="package" version="1.66">biopython</requirement> - <requirement type="package" version="1.4">matplotlib</requirement> - <requirement type="package" version="1.0">graphlan</requirement> - </requirements> + <macros> + <import>graphlan_macros.xml</import> + </macros> + + <expand macro="requirements"/> <stdio> + <regex match="Warning" + source="stderr" + level="warning" + description="" /> </stdio> <version_command> @@ -49,11 +53,9 @@ </command> <inputs> - <param name="input_tree" type="data" format="txt" label="Input tree in - PhlyloXML format" help=""/> + <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)"> + <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> @@ -97,23 +99,19 @@ <tests> <test> - <param name="input_tree" value="output_modified_tree.txt"/> - <param name='format' value="png"/> + <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" value="output_image.png" /> + <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. +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>`_. @@ -121,4 +119,4 @@ <citations> </citations> -</tool> \ No newline at end of file +</tool>
--- a/graphlan_annotate.xml Fri Apr 01 05:51:57 2016 -0400 +++ b/graphlan_annotate.xml Mon May 02 05:44:20 2016 -0400 @@ -1,14 +1,18 @@ -<tool id="graphlan_annotate" name="Modify an input tree for GraPhlAn" version="1.0"> +<tool id="graphlan_annotate" name="Generation, personalization and annotation of tree" version="0.9.7"> - <description></description> + <description>for GraPhlAn</description> - <requirements> - <requirement type="package" version="1.66">biopython</requirement> - <requirement type="package" version="1.4">matplotlib</requirement> - <requirement type="package" version="1.0">graphlan</requirement> - </requirements> + <macros> + <import>graphlan_macros.xml</import> + </macros> + + <expand macro="requirements"/> <stdio> + <regex match="Warning" + source="stderr" + level="warning" + description="" /> </stdio> <version_command> @@ -30,11 +34,9 @@ </command> <inputs> - <param name="input_tree" type="data" format="txt" label="Input tree" - help="Newick, Nexus, PhyloXML or plain text"/> + <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="(--annot)" optional="True"/> + <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> @@ -46,22 +48,18 @@ <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" /> + <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 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, ...). +`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>`_.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphlan_macros.xml Mon May 02 05:44:20 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/intermediary_tree.txt Mon May 02 05:44:20 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> + 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</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/test-data/output_modified_tree.txt Fri Apr 01 05:51:57 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,439 +0,0 @@ -<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> - 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<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> - 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<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> - 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<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 Fri Apr 01 05:51:57 2016 -0400 +++ b/tool_dependencies.xml Mon May 02 05:44:20 2016 -0400 @@ -6,7 +6,7 @@ <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="graphlan" version="1.0"> + <package name="graphlan" version="1.0.0"> <install version="1.0"> <actions> <action type="shell_command">