comparison iqtree.xml @ 3:973a28be3b7f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"

2:d1c340a5664b

<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.1" >
    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />

            <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">
                            <sanitizer>
                                <valid initial="string.ascii_uppercase,+" />
                            </sanitizer>
                        </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[

                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
IQ-TREE
=======

3:973a28be3b7f

<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.3" >
    <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
    <macros>
        <import>iqtree_macros.xml</import>
    </macros>
    <expand macro="requirements" />

            <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[

                <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>
                    <has_text_matching expression=".*Human.*Whale.*" />
                </assert_contents>
            </output>
            <output name='treefile'>
                <assert_contents>
                    <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
IQ-TREE
=======