view data_manager/data_manager_fetch_and_index_maf.xml @ 0:aed50ca398bb draft

"planemo upload for repository commit 9c8e61ce03ebd67c2c852f5db4a62d19200c77fe"
author iuc
date Thu, 25 Jun 2020 14:02:25 -0400
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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 UCSC</description>
        <requirement type="package" version="3.7">python</requirement>
        <requirement type="package" version="0.8.8">bx-python</requirement>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/' --nexus '$nexus'
        --name '$name' --output '$output' --dbkey '${dbkey.fields.dbkey}'
        <param name="dbkey" type="select" label="Species aligned against">
            <options from_data_table="all_fasta"/>
        <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" />
        <data name="output" format="data_manager_json" metadata_source="dbkey" />
**What it does**

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