<tool id="ete_homology_classifier" name="Homology Classifier and Filter" version="@VERSION@">
    <description>from a genetree using the ETE Toolkit</description>
    <macros>
        <import>ete_macros.xml</import>
        <xml name="homologies_macro" token_label="" token_help="">
            <param name="homologies" type="select" multiple="true" optional="false" display="checkboxes" label="@LABEL@" help="@HELP@">
                <option value="one-to-one" selected="true">one-to-one</option>
                <option value="one-to-many" selected="true">one-to-many</option>
                <option value="many-to-one" selected="true">many-to-one</option>
                <option value="many-to-many" selected="true">many-to-many</option>
                <option value="paralogs" selected="true">Paralogs</option>
            </param>
        </xml>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
python '$__tool_directory__/ete_homology_classifier.py'
--genetree '$genetreeFile'
--out_format '$format_type.out_format'
#if $format_type.homologies:
    --filters $format_type.homologies
#end if
> $homology
    ]]>
    </command>
    <inputs>
        <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" />
        <conditional name="format_type">
            <param name="out_format" type="select" label="Output format">
                <option value="tabular" selected="true">Tabular</option>
                <option value="csv">One-line CSV</option>
            </param>
            <when value="tabular">
                <expand macro="homologies_macro" label="Pair types to keep"/>
            </when>
            <when value="csv">
                <expand macro="homologies_macro" label="Allowed homology types for the GeneTree" help="If the GeneTree contains any other homology type, then the output will be empty" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="homology" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="format_type.out_format" value="csv" format="csv" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="genetreeFile" ftype="nhx" value="genetree.nhx" />
            <param name="out_format" value="tabular"/>
            <param name="homologies" value="one-to-one,one-to-many,many-to-one,many-to-many,paralogs" />
            <output name="homology" file="11_homology.tabular" />
        </test>
        <test>
            <param name="genetreeFile" ftype="nhx" value="11_genetree.nhx" />
            <param name="out_format" value="csv"/>
            <output name="homology" file="11_homology.csv" />
        </test>
    </tests>
    <help>
    <![CDATA[
Classify and filter Homology from single GeneTree by utilising the `ETE Toolkit`_.

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

**Output format:**

*tabular*:

======================  ========================  ============
       gene_1                  gene_2               homology
======================  ========================  ============
insr_rattusnorvegicus   insr_musmusculus          one-to-one
insr_rattusnorvegicus   insr_homosapiens          one-to-one
insr_rattusnorvegicus   insr_pantroglodytes       one-to-one
insr_rattusnorvegicus   insr_susscrofa            one-to-one
insr_musmusculus        insr_homosapiens          one-to-one
insr_musmusculus        insr_pantroglodytes       one-to-one
insr_musmusculus        insr_susscrofa            one-to-one
insr_homosapiens        insr_pantroglodytes       one-to-one
insr_homosapiens        insr_susscrofa            one-to-one
insr_pantroglodytes     insr_susscrofa            one-to-one
======================  ========================  ============

\

*One-line CSV*::

    insr_rattusnorvegicus,insr_musmusculus,insr_homosapiens,insr_pantroglodytes,insr_susscrofa
    ]]>
    </help>
    <expand macro="citations" />
</tool>