Mercurial > repos > iuc > graphlan_annotate
changeset 1:cf1df6b2220a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit b5bd1ab6e4f3a14819dbc2bdad33006bc6131b3c"
author | iuc |
---|---|
date | Fri, 24 Jan 2020 16:25:56 -0500 |
parents | 5d6f8f0bef7c |
children | 97e3b735ed22 |
files | graphlan_annotate.xml graphlan_macros.xml test-data/intermediary_tree |
diffstat | 3 files changed, 152 insertions(+), 151 deletions(-) [+] |
line wrap: on
line diff
--- a/graphlan_annotate.xml Sat Mar 04 10:27:20 2017 -0500 +++ b/graphlan_annotate.xml Fri Jan 24 16:25:56 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="graphlan_annotate" name="Generation, personalization and annotation of tree" version="@WRAPPER_VERSION@.0"> +<tool id="graphlan_annotate" name="Generation, personalization and annotation of tree" version="@WRAPPER_VERSION@"> <description>for GraPhlAn</description> <macros> <import>graphlan_macros.xml</import> @@ -48,4 +48,4 @@ ]]></help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>
--- a/graphlan_macros.xml Sat Mar 04 10:27:20 2017 -0500 +++ b/graphlan_macros.xml Fri Jan 24 16:25:56 2020 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.0.0</token> + <token name="@WRAPPER_VERSION@">1.1.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">graphlan</requirement> @@ -11,4 +11,4 @@ <citation type="doi">10.7717/peerj.1029</citation> </citations> </xml> -</macros> \ No newline at end of file +</macros>
--- a/test-data/intermediary_tree Sat Mar 04 10:27:20 2017 -0500 +++ b/test-data/intermediary_tree Fri Jan 24 16:25:56 2020 -0500 @@ -46,6 +46,41 @@ <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__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__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> @@ -66,11 +101,6 @@ <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> @@ -80,6 +110,11 @@ <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">21.1340492974</property> </clade> </clade> + <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> </clade> </clade> @@ -91,36 +126,6 @@ <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> @@ -180,16 +185,6 @@ <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> @@ -199,39 +194,44 @@ <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">25.9449465996</property> </clade> </clade> + <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> </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> + <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">22.66961905</property> + <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property> <clade> - <name>o__Actinomycetales</name> + <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">22.66961905</property> + <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property> <clade> - <name>f__Propionibacteriaceae</name> + <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">22.66961905</property> + <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property> <clade> - <name>g__Propionibacterium</name> + <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">22.66961905</property> + <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property> <clade> - <name>s__Propionibacterium_acnes</name> + <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">22.66961905</property> + <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property> <clade> - <name>t__Propionibacterium_acnes_unclassified</name> + <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">22.66961905</property> + <property applies_to="clade" datatype="xsd:string" id_ref="clade_marker_size" ref="A:1">26.8159954288</property> </clade> </clade> </clade> @@ -245,91 +245,6 @@ <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> @@ -419,6 +334,91 @@ </clade> </clade> </clade> + <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_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> + <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> + </clade> + </clade> + </clade> </clade> </clade> </clade> @@ -434,6 +434,7 @@ <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="leg_clade_marker_shape" ref="A:1">._._._.</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