view data_manager/data_manager_fetch_and_index_maf.xml @ 0:475b10cd2ae8 draft default tip

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<tool id="data_manager_fetch_and_index_maf" name="Fetch and index" version="1.0.0" tool_type="manage_data" profile="19.01">
    <description>multiple alignments from NCBI</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
        <requirement type="package" version="0.8.8">bx-python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/data_manager_fetch_and_index_maf.py' --nexus '$nexus'
        --alignments '$alignments' --name '$name' --output '$output'
    ]]></command>
    <inputs>
        <param name="dbkey" type="select" label="Species aligned against">
            <options from_data_table="all_fasta"/>
        </param>
        <param name="nexus" type="text" label="FTP path to nexus file on UCSC." help="The MAF paths will be computed from this" />
        <param name="name" type="text" label="Display name for this multi-alignment" />
    </inputs>
    <outputs>
        <data name="output" format="data_manager_json"/>
    </outputs>
    <tests>
        <test />
    </tests>
    <help>
**What it does**

Fetches a multiple alignment from UCSC's FTP server and indexes it with bx-python.

------

.. class:: infomark

**Notice:** If you leave name, description, or id blank, it will be generated automatically.
    </help>
</tool>