comparison data_manager/data_manager_mitos.xml @ 0:6d384a5c22bf draft

"planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_mitos commit 0bc221dedfb465eb591080bf71a8f05d5cd81ce3-dirty"

0:6d384a5c22bf

<?xml version="1.0"?>
<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1">
    <description>reference data downloader</description>
    <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="refseq39">RefSeq39 (equivalent to MITOS1 data)</option>
                    <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>
                </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>
    </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

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
    </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>