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comparison iqtree.xml @ 13:24d024316465 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 25f53344278285ac5e75ac902aec60a38921aa12
author iuc
date Tue, 09 Apr 2024 05:10:40 +0000
parents 9b892d7f82cc
children 70acec670c30
comparison
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12:9b892d7f82cc 13:24d024316465
1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > 1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description> 2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
3 <macros> 3 <macros>
4 <import>iqtree_macros.xml</import> 4 <import>iqtree_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/>
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 iqtree 9 iqtree
9 --prefix PREF 10 --prefix PREF
10 #if $general_options.short_alignments: 11 #if $general_options.short_alignments:
422 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/> 423 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
423 </section> 424 </section>
424 <section name="modelling_parameters" title="Modelling Parameters"> 425 <section name="modelling_parameters" title="Modelling Parameters">
425 <section name="automatic_model" expanded="False" title="Automatic model selection"> 426 <section name="automatic_model" expanded="False" title="Automatic model selection">
426 <conditional name="cond_model" > 427 <conditional name="cond_model" >
427 <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/> 428
429 <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models">
430 <option value="true" selected="True">Yes, I want to use a custom model</option>
431 <option value="false">No, a custom model is not needed</option>
432 </param>
428 <when value="true"> 433 <when value="true">
429 <param argument="-m" type="text" label="Model"> 434 <param argument="-m" type="text" label="Model">
430 <expand macro="sanitize_query" 435 <expand macro="sanitize_query"
431 validinitial="string.ascii_uppercase,string.digits,string.punctuation" /> 436 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
432 </param> 437 </param>
433 </when> 438 </when>
434 <when value="false"> 439 <when value="false">
435 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" > 440 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
436 <help><![CDATA[ 441 <help><![CDATA[
437 <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/> 442 <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/>
438 IQ-TREE also works for codon, binary and morphogical data. 443 IQ-TREE also works for codon, binary and morphological data.
439 <table> 444 <table>
440 <tr> 445 <tr>
441 <td><i>TESTONLY</i></td> 446 <td><i>TESTONLY</i></td>
442 <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td> 447 <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td>
443 </tr> 448 </tr>
767 <param name="sup_min" value="0.0" /> 772 <param name="sup_min" value="0.0" />
768 <param name="nmax" value="1000" /> 773 <param name="nmax" value="1000" />
769 <param name="bcor" value="0.99" /> 774 <param name="bcor" value="0.99" />
770 <param name="nstep" value="100" /> 775 <param name="nstep" value="100" />
771 <param name="beps" value="0.5" /> 776 <param name="beps" value="0.5" />
772 <param name="b" value="2" />
773 <output name="iqtree"> 777 <output name="iqtree">
774 <assert_contents> 778 <assert_contents>
775 <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" /> 779 <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" />
776 </assert_contents> 780 </assert_contents>
777 </output> 781 </output>
801 <param name="sup_min" value="0.0" /> 805 <param name="sup_min" value="0.0" />
802 <param name="nmax" value="1000" /> 806 <param name="nmax" value="1000" />
803 <param name="bcor" value="0.99" /> 807 <param name="bcor" value="0.99" />
804 <param name="nstep" value="100" /> 808 <param name="nstep" value="100" />
805 <param name="beps" value="0.5" /> 809 <param name="beps" value="0.5" />
806 <!-- <param name="b" value="100" /> -->
807 <output name="iqtree"> 810 <output name="iqtree">
808 <assert_contents> 811 <assert_contents>
809 <has_text_matching expression="GTR\+F\+I\+G4(\s+((-|\d|\.)+))+" /> 812 <has_text_matching expression="GTR\+F\+I\+G4(\s+((-|\d|\.)+))+" />
810 </assert_contents> 813 </assert_contents>
811 </output> 814 </output>
926 929
927 Running example 930 Running example
928 --------------------- 931 ---------------------
929 932
930 From the download_ there is an example alignment called `example.phy` 933 From the download_ there is an example alignment called `example.phy`
931 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals (Source: `Phylogenetic Handbook`_) 934 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals.
932 935
933 .. _`Phylogenetic Handbook` : http://www.kuleuven.be/aidslab/phylogenybook/home.html)).
934 .. _download: http://www.iqtree.org/#download 936 .. _download: http://www.iqtree.org/#download
935 937
936 You can now start to reconstruct a maximum-likelihood tree 938 You can now start to reconstruct a maximum-likelihood tree
937 from this alignment by entering (assuming that you are now in the same folder with `example.phy`): 939 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
938 940
1056 1058
1057 * **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment. 1059 * **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment.
1058 1060
1059 * **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. 1061 * **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.
1060 1062
1061 * **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. 1063 * **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.
1062 1064
1063 .. _SplitsTree: http://www.splitstree.org 1065 .. _IcyTree: https://icytree.org
1064 1066
1065 1067
1066 Reducing impact of severe model violations with UFBoot 1068 Reducing impact of severe model violations with UFBoot
1067 ------------------------------------------------------ 1069 ------------------------------------------------------
1068 1070