<tool id="ete_species_tree_generator" name="ETE species tree generator" version="@VERSION@.1">
    <description>from a list of species 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 '$__tool_directory__/ete_species_tree_generator.py'
-s '$speciesFile'
-d $database
-o '$outputFile'
#if $output_format.treebest == 'yes'
    -f 8
#else
    -f ${output_format.format_selector}
#end if
-t $output_format.treebest
    ]]>
    </command>
    <inputs>
        <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />
        <param name="database" type="data" format="sqlite" label="(ETE3) Taxonomy Database" help="The sqlite formatted Taxonomy used by ETE3 (which is derived from NCBI taxonomy)" />
        <conditional name="output_format">
            <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes" />
            <when value="no">
                <param name="format_selector" type="select" label="Output format" help="See table below">
                    <option value="0" selected="true">Flexible with support values (0)</option>
                    <option value="1">Flexible with internal node names (1)</option>
                    <option value="2">All branches + leaf names + internal supports (2)</option>
                    <option value="3">All branches + all names (3)</option>
                    <option value="4">Leaf branches + leaf names (4)</option>
                    <option value="5">Internal and leaf branches + leaf names (5)</option>
                    <option value="6">Internal branches + leaf names (6)</option>
                    <option value="7">Leaf branches + all names (7)</option>
                    <option value="8">All names (8)</option>
                    <option value="9">Leaf names (9)</option>
                    <option value="100">Topology only (100)</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="speciesFile" ftype="txt" value="species.txt" />
            <param name="database" ftype="sqlite" value="taxdump.sqlite" />
            <param name="treebest" value="yes" />
            <output name="outputFile">
                <assert_contents>
                    <has_text text="(Homosapiens*,Pantroglodytes*,Gorillagorillagorilla*)" />
                    <has_text text=")root;" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
    <![CDATA[
Generate a species tree from a list of species 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>