Mercurial > repos > dave > data_manager_fetch_index_maf

view data_manager/data_manager_fetch_and_index_maf.xml @ 1:edf39ed96bc3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit f8a19615cd097290a1239d4bb6b8eb52c9d73b03-dirty"
author dave
date Wed, 15 Jul 2020 15:50:54 -0400
parents de73b258a601
children
line wrap: on
line source

<tool id="data_manager_fetch_and_index_maf" name="Fetch and index" version="1.1.0" tool_type="manage_data" profile="19.01">
    <description>multiple alignments from UCSC</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'
        --name '$name' --output '$output' --dbkey '${dbkey.fields.dbkey}'
    ]]></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" metadata_source="dbkey" />
    </outputs>
    <help>
**What it does**

This data manager fetches a multiple alignment from UCSC's FTP server and indexes it with bx-python.
    </help>
</tool>