comparison data_manager/data_manager_mitos.xml @ 2:ae5ddc5a6511 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit b63133897598f2881de7bad1f18fcd69d7d7e9df-dirty"

1:7548eaf95697

<?xml version="1.0"?>
<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2">
    <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'

                    <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>

                <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

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>

2:ae5ddc5a6511

<?xml version="1.0"?>
<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2">
    <description>reference data downloader blah</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'

                    <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>

                <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

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>