view data_manager/motus_db_fetcher.xml @ 0:0370fe3cf518 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14

<?xml version="1.0"?>
<tool id="motus_db_fetcher" name="mOTUs DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Fetches the DB required for mOTUs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools" />
    <expand macro="requirements" />
    <!-- <expand macro="version" /> -->

    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/data_manager_fetch_motus_db.py' --out '${out_file}' --version '${version}' 
        $test_data_manager
    ]]>
    </command>
    <inputs>
    <param name="test_data_manager" type="hidden" truevalue="--test" falsevalue="" checked="False" label="Copy minimal test DB and create mock data table entry." />

    <!-- <param name="test_data_manager" type="text" value=""/> -->
    <param argument="--version" type="select" multiple="false" label="Database Version" help="Check https://zenodo.org/records/7778108 for current version. The default value is recommended.">
        <option value="3.1.0">3.1.0</option>
        <option value="3.0.1">3.0.1</option>
        <option value="3.0.0">3.0.0</option>
    </param>

    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>
    <tests>
    <test expect_num_outputs="1">
        <param name="test_data_manager" value="--test"/>
        <param name="version" value="3.1.0"/>
        <output name="out_file">
                <assert_contents>
                    <has_text text="mOTUs DB version 3.1.0 downloaded at"/>
                </assert_contents>
        </output>
    </test>
    </tests>
    <help><![CDATA[
mOTUs
=====

The mOTUs profiler is a tool designed for taxonomic profiling of metagenomic and metatranscriptomic data.
It allows for the identification and quantification of microbial community composition directly from sequencing reads. 
mOTUs utilizes a database of marker genes identified across a wide range of microbial taxa, enabling the detection of known and unknown microorganisms in your sample data.

Additional Resources
====================

For a more comprehensive understanding of mOTUs and detailed usage instructions, please visit the mOTUs GitHub repository:

mOTUs GitHub Repository: [https://github.com/motu-tool/mOTUs](https://github.com/motu-tool/mOTUs)
        
Data Manager
============

This DM download the available DBs from: https://zenodo.org/records/5012106
            ]]></help>
    <expand macro="citations" />
    <expand macro="creator" />
</tool>