annotate ete_genetree_splitter.xml @ 12:dc32007a6b36 draft

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

<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>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
    </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>
            <when value="False" />
            <when value="True">
                <param name="speciesFile" type="data" format="nhx" label="Species file" help="Species Tree in nhx format" />
                <param name="species_format" type="select" label="Input species tree format" help="See table below">
                    <option value="0">Flexible with support values (0)</option>
                    <option value="1">Flexible with internal node names (1)</option>
                    <option value="2">All branches + leaf names + internal supports (2)</option>
                    <option value="3">All branches + all names (3)</option>
                    <option value="4">Leaf branches + leaf names (4)</option>
                    <option value="5">Internal and leaf branches + leaf names (5)</option>
                    <option value="6">Internal branches + leaf names (6)</option>
                    <option value="7">Leaf branches + all names (7)</option>
                    <option value="8" selected="true">All names (8)</option>
                    <option value="9">Leaf names (9)</option>
                    <option value="100">Topology only (100)</option>
                </param>
             </when>
        </conditional> 
        
        <param name="output_format" type="select" label="Output GeneTree format" help="See table below">
            <option value="0">Flexible with support values (0)</option>
            <option value="1">Flexible with internal node names (1)</option>
            <option value="2">All branches + leaf names + internal supports (2)</option>
            <option value="3">All branches + all names (3)</option>
            <option value="4">Leaf branches + leaf names (4)</option>
            <option value="5">Internal and leaf branches + leaf names (5)</option>
            <option value="6">Internal branches + leaf names (6)</option>
            <option value="7">Leaf branches + all names (7)</option>
            <option value="8">All names (8)</option>
            <option value="9" selected="true">Leaf names (9)</option>
            <option value="100">Topology only (100)</option>
        </param> 
    </inputs>
    <outputs>
        <collection name="genetrees_lists" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_genetree\.nhx" ext="nhx" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
            <param name="gene_node" value="0"/>
            <param name="splitter" value="dups"/>
            <param name="output_format" value="9" />
            <output_collection name="genetrees_lists" type="list" count="4">
                <element name="1" file="11_genetree.nhx" ftype="nhx" />
                <element name="2" file="12_genetree.nhx" ftype="nhx" />
                <element name="3" file="13_genetree.nhx" ftype="nhx" />
                <element name="4" file="14_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="dups"/>
            <param name="gainlose" value="True" />
            <param name="speciesFile" ftype="nhx" value="speciestree.nhx" />
            <param name="species_format" value="8" />
            <param name="output_format" value="9" />
            <output_collection name="genetrees_lists" type="list" count="5">
                <element name="1" file="21_genetree.nhx" ftype="nhx" />
                <element name="2" file="22_genetree.nhx" ftype="nhx" />
                <element name="3" file="23_genetree.nhx" ftype="nhx" />
                <element name="4" file="24_genetree.nhx" ftype="nhx" />
                <element name="5" file="25_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="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`_.

.. _ETE Toolkit: http://etetoolkit.org/

**Output format:**

======= ============================================= ========================================================================================
FORMAT  DESCRIPTION                                     SAMPLE
------- --------------------------------------------- ----------------------------------------------------------------------------------------
0       flexible with support values                    ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
1       flexible with internal node names               ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
2       all branches + leaf names + internal supports   ((D:0.723274,F:0.567784)1.000000:0.067192,(B:0.279326,H:0.756049)1.000000:0.807788);
3       all branches + all names                        ((D:0.723274,F:0.567784)E:0.067192,(B:0.279326,H:0.756049)B:0.807788);
4       leaf branches + leaf names                      ((D:0.723274,F:0.567784),(B:0.279326,H:0.756049));
5       internal and leaf branches + leaf names         ((D:0.723274,F:0.567784):0.067192,(B:0.279326,H:0.756049):0.807788);
6       internal branches + leaf names                  ((D,F):0.067192,(B,H):0.807788);
7       leaf branches + all names                       ((D:0.723274,F:0.567784)E,(B:0.279326,H:0.756049)B);
8       all names                                       ((D,F)E,(B,H)B);
9       leaf names                                      ((D,F),(B,H));
100     topology only                                   ((,),(,));
======= ============================================= ========================================================================================
    ]]></help>
    <expand macro="citations" />
</tool>