comparison iqtree.xml @ 6:224c75ad0518 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"

5:fc06db7794f1

#if str($tree_parameters.generating_random.r) != ''
    -r '$tree_parameters.generating_random.r'
#end if

$tree_parameters.generating_random.r
$tree_parameters.generating_random.rand


#if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
    --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
#end if

                                    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)" >
                            <option value="" selected="true">(None)</option>
                            <option value="TESTONLY">Standard model selection</option>
                            <option value="TEST">Standard model selection followed by tree inference</option>
                            <option value="MF">Extended model selection with FreeRate heterogeneity</option>
                            <option value="MFP">Extended model selection followed by tree inference</option>

                <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" />

            </section>
            <section name="generating_random" expanded="False" title="Generating random trees">
                <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
                <param argument="--rand" type="boolean" truevalue="--rand UNI" falsevalue="" checked="false" label="Like -r, but a random tree is created under uniform model."/>
                <param argument="--rand" type="boolean" truevalue="--rand CAT" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/>
                <param argument="--rand" type="boolean" truevalue="--rand BAL" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/>
                <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
                <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
                <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
            </section>
            <section name="ancestral_state" title="Ancestral State Reconstruction">

        <data name="mlrate" format="data" from_work_dir="*.mlrate" label="">
            <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TEST" />
            <param name="msub" value="nuclear" />

                    <has_line line="BEGIN Splits;" />
                    <has_line line="END; [Splits]" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- bootstrap sans model -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <!-- <param name="m" value="TESTONLY" /> -->

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- model sans bootstrap -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TESTONLY" />

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="s" value="example.phy" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="s" value="example.phy" />
            <param name="opt_custommodel" value="true" />
            <param name="m" value="GTR+G{0.9}" />
            <output name="iqtree">
                <assert_contents>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="s" value="short.fasta" />
            <param name="short_alignments" value="true" />
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />

6:224c75ad0518

#if str($tree_parameters.generating_random.r) != ''
    -r '$tree_parameters.generating_random.r'
#end if

#if $tree_parameters.generating_random.rand
    $tree_parameters.generating_random.rand
#end if

#if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
    --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
#end if

                                    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>
    <tr>
        <td><i>TEST</i></td>
        <td>Like -m TESTONLY but immediately followed by tree reconstruction using the best-fit model found. So this performs both model selection and tree inference within a single run.</td>
    </tr>
    <tr>
        <td><i>MF</i></td>
        <td>Best-fit model selection without tree reconstruction.</td>
    </tr>
    <tr>
        <td><i>MFP</i></td>
        <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td>
    </tr>
</table>
]]>
                            </help>
                            <option value="" selected="true">(None)</option>
                            <option value="TESTONLY">Standard model selection</option>
                            <option value="TEST">Standard model selection followed by tree inference</option>
                            <option value="MF">Extended model selection with FreeRate heterogeneity</option>
                            <option value="MFP">Extended model selection followed by tree inference</option>

                <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" />

            </section>
            <section name="generating_random" expanded="False" title="Generating random trees">
                <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
                <param argument="--rand" type="select" optional="true" label="Random tree creation">
                    <option value="--rand UNI">Uniform model</option>
                    <option value="--rand CAT">Random caterpillar tree</option>
                    <option value="--rand BAL">Random balanced tree</option>
                </param>
                <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
                <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
                <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
            </section>
            <section name="ancestral_state" title="Ancestral State Reconstruction">

        <data name="mlrate" format="data" from_work_dir="*.mlrate" label="">
            <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="6">
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TEST" />
            <param name="msub" value="nuclear" />

                    <has_line line="BEGIN Splits;" />
                    <has_line line="END; [Splits]" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <!-- bootstrap sans model -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <!-- <param name="m" value="TESTONLY" /> -->

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <!-- model sans bootstrap -->
            <param name="seed" value="1257" />
            <param name="seqtype" value="AA" />
            <param name="s" value="example.phy" />
            <param name="m" value="TESTONLY" />

                <assert_contents>
                    <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="s" value="example.phy" />
            <output name="iqtree">
                <assert_contents>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="s" value="example.phy" />
            <param name="opt_custommodel" value="true" />
            <param name="m" value="GTR+G{0.9}" />
            <output name="iqtree">
                <assert_contents>

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="s" value="short.fasta" />
            <param name="short_alignments" value="true" />
            <output name="treefile">
                <assert_contents>
                    <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />