diff iqtree.xml @ 13:24d024316465 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12

--- a/iqtree.xml	Sat Nov 27 09:45:09 2021 +0000
+++ b/iqtree.xml	Tue Apr 09 05:10:40 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>iqtree_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 iqtree
@@ -424,7 +425,11 @@
         <section name="modelling_parameters" title="Modelling Parameters">
             <section name="automatic_model" expanded="False" title="Automatic model selection">
                 <conditional name="cond_model" >
-                    <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/>
+
+                    <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models">
+                        <option value="true" selected="True">Yes, I want to use a custom model</option>
+                        <option value="false">No, a custom model is not needed</option>
+                    </param>
                     <when value="true">
                         <param argument="-m" type="text" label="Model">
                             <expand macro="sanitize_query"
@@ -435,7 +440,7 @@
                         <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
                             <help><![CDATA[
 <b>Note:</b> Only <code>TEST</code> and custom models that do not rely on <code>MF</code> can be used in conjunction with bootstrap parameters (-b)<br/><br/>
-IQ-TREE also works for codon, binary and morphogical data.
+IQ-TREE also works for codon, binary and morphological data.
 <table>
     <tr>
         <td><i>TESTONLY</i></td>
@@ -769,7 +774,6 @@
             <param name="bcor" value="0.99" />
             <param name="nstep" value="100" />
             <param name="beps" value="0.5" />
-            <param name="b" value="2" />
             <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" />
@@ -803,7 +807,6 @@
             <param name="bcor" value="0.99" />
             <param name="nstep" value="100" />
             <param name="beps" value="0.5" />
-            <!-- <param name="b" value="100" /> -->
             <output name="iqtree">
                 <assert_contents>
                     <has_text_matching expression="GTR\+F\+I\+G4(\s+((-|\d|\.)+))+" />
@@ -928,9 +931,8 @@
 ---------------------
 
 From the download_ there is an example alignment called `example.phy`
-in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_)
+in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals.
 
-.. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)).
 .. _download: http://www.iqtree.org/#download
 
 You can now start to reconstruct a maximum-likelihood tree
@@ -1058,9 +1060,9 @@
 
 * **example.phy.splits**: support values in percentage for all splits (bipartitions), computed as the occurence frequencies in the bootstrap trees. This file is in "star-dot" format.
 
-* **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program SplitsTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
+* **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program IcyTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
 
-.. _SplitsTree: http://www.splitstree.org
+.. _IcyTree: https://icytree.org
 
 
 Reducing impact of severe model violations with UFBoot