<?xml version="1.0"?>
<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.3" profile="23.0">
    <description>reference data downloader</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[
    python '$__tool_directory__/data_manager.py' 
    --out '${out_file}'
    --type '$type_cond.type_select'
    --db '$type_cond.database'
    ]]>
    </command>
    <inputs>
        <conditional name="type_cond">
            <param name="type_select" type="select" label="MITOS version">
                <option value="mitos">MITOS</option>
                <option value="mitos2">MITOS2</option>
            </param>
            <when value="mitos">
                <param name="database" type="select" label="Reference data version">
                    <option value="mitos1-refdata">RefSeq39 + MiTFi tRNA models</option>
                </param>
            </when>
            <when value="mitos2">
                <param name="database" type="select" label="Reference data version">
                    <option value="refseq63m">RefSeq63 Metazoa</option>
                    <option value="refseq63f">RefSeq63 Fungi</option>
                    <option value="refseq63o">RefSeq63 Opisthokonta</option>
                    <option value="refseq89m">RefSeq89 Metazoa</option>
                    <option value="refseq89f">RefSeq89 Fungi</option>
                    <option value="refseq89o">RefSeq89 Opisthokonta</option>
                    <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <conditional name="type_cond">
                <param name="type_select" value="mitos"/>
                <param name="database" value="mitos1-refdata"/>
            </conditional>
            <output name="out_file" file="mitos_refseq39.json"/>
        </test>
        <test>
            <conditional name="type_cond">
                <param name="type_select" value="mitos2"/>
                <param name="database" value="refseq63m"/>
            </conditional>
            <output name="out_file" file="mitos2_refseq63.json"/>
        </test>
    </tests>
    <help>
This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.

For MITOS the reference data includes 

- protein data bases derived from RefSeq release 39 (see Bernt et al. 2012)
- covariance models for tRNAs and rRNAs as described in Jühling et al 2012

Data is downloaded from https://zenodo.org/record/2683856.

For MITOS2 the reference data sets are available for three different taxons

- Metazoa
- Fungi
- Opisthokonta

these have been computed for RefSeq release 63 and 89. In addition the reference data 
for MITOS1 has been converted to be usable in MITOS2.
contains

The reference data sets contain: 

- protein data bases derived from the corresponding RefSeq release Donath et al. 2019
- covariance models computed for the data in the RefSeq releas based on the MITOS1 models 
- in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017

Data is downloaded from https://zenodo.org/record/4284483.
    </help>
    <citations>
        <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
        <citation type="doi">10.1093/nar/gkr1131</citation>
        <citation type="doi">10.1016/j.ympev.2016.09.024</citation>
        <citation type="doi">10.1093/nar/gkz833</citation>
    </citations>
</tool>