Mercurial > repos > iuc > graphlan_annotate

changeset 1:cf1df6b2220a draft

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"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