comparison ete_genetree_splitter.xml @ 12:dc32007a6b36 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit c568584f1eaa1366603b89db7e52994812f5d387

11:2db72467da51

<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@">
    <description>from a genetree using the ETE Toolkit</description>
    <macros>
        <import>ete_macros.xml</import>
    </macros>
    <expand macro="requirements" />

    </stdio>
    <command><![CDATA[
python '$__tool_directory__/ete_genetree_splitter.py'
--genetree '$genetreeFile'
--gene_node $gene_node
--split $splitter
#if $gainlose_conditional.gainlose == "True"
    --speciestree '$gainlose_conditional.speciesFile'
    --species_format $gainlose_conditional.species_format
    --gainlose
#end if
--output_format $output_format
    ]]></command>
    <inputs>
        <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" />
         <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option">
            <option value="0" selected="true">gene_species</option>
            <option value="1">species_gene</option>
        </param>
        <param name="splitter" type="select" label="GeneTree splitting algorithm">
            <option value="dups">Split by Duplication</option>
            <option value="treeko">Split using TreeKO algorithm</option>
        </param>
        <conditional name="gainlose_conditional">
            <param name="gainlose" type="select" label="Find out gene gain/lose">
                <option value="True">Yes</option>
                <option value="False" selected="true">No</option>
            </param>

        <test>
            <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
            <param name="gene_node" value="0"/>
            <param name="splitter" value="treeko"/>
            <param name="output_format" value="9" />
            <output_collection name="genetrees_lists" type="list" count="5">
                <element name="1" file="31_genetree.nhx" ftype="nhx" />
                <element name="2" file="32_genetree.nhx" ftype="nhx" />
                <element name="3" file="33_genetree.nhx" ftype="nhx" />
                <element name="4" file="34_genetree.nhx" ftype="nhx" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.

12:dc32007a6b36

<tool id="ete_genetree_splitter" name="ETE GeneTree splitter" version="@VERSION@+galaxy1">
    <description>from a genetree using the ETE Toolkit</description>
    <macros>
        <import>ete_macros.xml</import>
    </macros>
    <expand macro="requirements" />

    </stdio>
    <command><![CDATA[
python '$__tool_directory__/ete_genetree_splitter.py'
--genetree '$genetreeFile'
--gene_node $gene_node
--split $splitting_conditional.splitter
#if $gainlose_conditional.gainlose == "True"
    --speciestree '$gainlose_conditional.speciesFile'
    --species_format $gainlose_conditional.species_format
    --gainlose
#end if
#if $splitting_conditional.splitter == "species"
    --ingroup '$splitting_conditional.ingroup'
    --outgroup '$splitting_conditional.outgroup'
#end if
--output_format $output_format
    ]]></command>
    <inputs>
        <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format" />
        <param name="gene_node" type="select" label="Select Gene node format" help="Select Gene node format from one of the option">
            <option value="0" selected="true">gene_species</option>
            <option value="1">species_gene</option>
        </param>
        <conditional name="splitting_conditional">
            <param name="splitter" type="select" label="GeneTree splitting algorithm">
                <option value="dups">Split by Duplication</option>
                <option value="treeko">Split using TreeKO algorithm</option>
                <option value="species">Split using In-group and Out-group species</option>
            </param>
            <when value="dups" />
            <when value="treeko" />
            <when value="species">
                <param name="ingroup" type="text" label="In-group species list" help="Comma-separated species list without whitespaces or special characters" />
                <param name="outgroup" type="text" label="Out-group species list" help="Comma-separated species list without whitespaces or special characters" />
            </when>
        </conditional>
        <conditional name="gainlose_conditional">
            <param name="gainlose" type="select" label="Find out gene gain/lose">
                <option value="True">Yes</option>
                <option value="False" selected="true">No</option>
            </param>

        <test>
            <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
            <param name="gene_node" value="0"/>
            <param name="splitter" value="treeko"/>
            <param name="output_format" value="9" />
            <output_collection name="genetrees_lists" type="list" count="4">
                <element name="1" file="31_genetree.nhx" ftype="nhx" />
                <element name="2" file="32_genetree.nhx" ftype="nhx" />
                <element name="3" file="33_genetree.nhx" ftype="nhx" />
                <element name="4" file="34_genetree.nhx" ftype="nhx" />
            </output_collection>
        </test>

        <test>
            <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
            <param name="gene_node" value="0"/>
            <param name="splitter" value="species"/>
            <param name="ingroup" value="pantroglodytes,homosapiens,rattusnorvegicus,musmusculus,canisfamiliaris" />
            <param name="outgroup" value="susscrofa" />
            <param name="output_format" value="9" />
            <output_collection name="genetrees_lists" type="list" count="4">
                <element name="1" file="41_genetree.nhx" ftype="nhx" />
                <element name="2" file="42_genetree.nhx" ftype="nhx" />
                <element name="3" file="43_genetree.nhx" ftype="nhx" />
                <element name="4" file="44_genetree.nhx" ftype="nhx" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Split GeneTrees from single GeneTree by duplication event using the `ETE Toolkit`_.