comparison iqtree.xml @ 13:24d024316465 draft

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

12:9b892d7f82cc

<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
iqtree
    --prefix PREF
    #if $general_options.short_alignments:

            <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
        </section>
        <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"/>
                    <when value="true">
                        <param argument="-m" type="text" label="Model">
                            <expand macro="sanitize_query"
                                    validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
                        </param>
                    </when>
                    <when value="false">
                        <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.
<table>
    <tr>
        <td><i>TESTONLY</i></td>
        <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>
    </tr>

            <param name="sup_min" value="0.0" />
            <param name="nmax" value="1000" />
            <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|\.)+))+" />
                </assert_contents>
            </output>

            <param name="sup_min" value="0.0" />
            <param name="nmax" value="1000" />
            <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|\.)+))+" />
                </assert_contents>
            </output>

Running example
---------------------

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`_)

.. _`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
from this alignment by entering (assuming that you are now in the same folder with `example.phy`):

* **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized  on the original alignment.

* **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.

.. _SplitsTree: http://www.splitstree.org


Reducing impact of severe model violations with UFBoot
------------------------------------------------------

13:24d024316465

<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
iqtree
    --prefix PREF
    #if $general_options.short_alignments:

            <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
        </section>
        <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="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"
                                    validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
                        </param>
                    </when>
                    <when value="false">
                        <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 morphological data.
<table>
    <tr>
        <td><i>TESTONLY</i></td>
        <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>
    </tr>

            <param name="sup_min" value="0.0" />
            <param name="nmax" value="1000" />
            <param name="bcor" value="0.99" />
            <param name="nstep" value="100" />
            <param name="beps" value="0.5" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>

            <param name="sup_min" value="0.0" />
            <param name="nmax" value="1000" />
            <param name="bcor" value="0.99" />
            <param name="nstep" value="100" />
            <param name="beps" value="0.5" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression="GTR\+F\+I\+G4(\s+((-|\d|\.)+))+" />
                </assert_contents>
            </output>

Running example
---------------------

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.

.. _download: http://www.iqtree.org/#download

You can now start to reconstruct a maximum-likelihood tree
from this alignment by entering (assuming that you are now in the same folder with `example.phy`):

* **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized  on the original alignment.

* **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 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.

.. _IcyTree: https://icytree.org


Reducing impact of severe model violations with UFBoot
------------------------------------------------------