<?xml version="1.0"?>
<tool id="gene_annotation_fetcher_data_manager" name="Gene Annotation Fetch" tool_type="manage_data" version="1.0.0">
    <description>gene annotation fetcher</description>
    <stdio>
        <exit_code description="Error" level="fatal" range="1:" />
    </stdio>
    <command interpreter="python">
    <![CDATA[
        data_manager.py --out "${out_file}"
        #if $gene_annotation_url:
            --url "${gene_annotation_url}"
        #end if
        #if $database_name:
            --name "${database_name}"
        #end if
    ]]>
    </command>
    <inputs>
        <param help="Enter a unique identifier, or leave blank for an auto-generated uuid" label="Name for this database" name="database_name" type="text" optional="True" />
        <param label="Enter URL for gene annotation files" name="gene_annotation_url" type="text" optional="False"/>
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>
    <tests>
        <test>
            <param name="database_name" value="cool_name"/>
            <param name="gene_annotation_url" value="http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf"/>
            <output name="out_file" file="../test-data/gene_annotation_out.json" compare="contains"/>
            <extra_files type="file" name="chr1-hg19_genes.gtf" value="chr1-hg19_genes.gtf"/>
        </test>
    </tests>
</tool>