<tool id="species_tree_generator" name="Species tree generator" version="3.0.0b35">
    <description>from a list of species using the ETE Toolkit</description>
     <requirements>
        <requirement type="package" version="3.0.0b35">ete3</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
    </stdio>
    <command>
    <![CDATA[
python $__tool_directory__/ete_tree_generator.py 
-s '$speciesFile'
#if $output_format.treebest == 'yes'
    -f 8
#else
    -f ${output_format.format_selector}
#end if
-t $output_format.treebest
-d $database
    ]]>
    </command>
    <inputs>
        <param name="speciesFile" type="data" format="txt" label="Species file" help="List with one species per line" />        
        <conditional name="output_format">
            <param name="treebest" type="select" label="Use in TreeBest" help="Select yes if specie tree to be used in TreeBest">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes" />
            <when value="no">
                <param name="format_selector" type="select" label="Output format" help="See table below">
                    <option value="0" selected="true">Flexible with support values (0)</option>
                    <option value="1">Flexible with internal node names (1)</option>
                    <option value="2">All branches + leaf names + internal supports (2)</option>
                    <option value="3">All branches + all names (3)</option>
                    <option value="4">Leaf branches + leaf names (4)</option>
                    <option value="5">Internal and leaf branches + leaf names (5)</option>
                    <option value="6">Internal branches + leaf names (6)</option>
                    <option value="7">Leaf branches + all names (7)</option>
                    <option value="8">All names (8)</option>
                    <option value="9">Leaf names (9)</option>
                    <option value="100">Topology only (100)</option>
                </param>
            </when>
        </conditional>
        <param name="database" type="select" label="Update database" help="Update database from NCBI (slower)">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
        </param>
    </inputs>
    <outputs>
        <data format="nhx" name="outputFile" label="${tool.name} on ${on_string}" from_work_dir="newickTree.nhx"/>
    </outputs>
    <tests>
        <test>
            <param name="speciesFile" ftype="txt" value="species.txt" />
            <param name="treebest" value="yes" />
            <output name="outputFile" file="out.nhx" />
        </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>
    <citations>
        <citation type="doi">10.1093/molbev/msw046</citation>
    </citations>
</tool>