view data_manager_monorail_index/data_manager/monorail_index_fetcher.xml @ 1:014bed8546e9 draft

Uploaded

<?xml version="1.0"?>
<tool id="monorail_index_fetcher" name="Monorail Index Fetch" tool_type="manage_data" version="1.0.0">
    <description>monorail indexes fetcher</description>
    <stdio>
        <exit_code description="Error" level="fatal" range="1:" />
    </stdio>
    <command><![CDATA[
        #import os
        #set $target_directory = str($out_file.extra_files_path)
        #set $subdir = os.path.basename($target_directory)
        mkdir '${target_directory}' &&
        bash '${__tool_directory__}/download_and_extract_monorail_index.sh' '${target_directory}' '${monorail_index_url}' &&
        python '${__tool_directory__}/data_manager.py' --out "${out_file}"
        #if $monorail_index_url:
            --url "${monorail_index_url}"
        #end if
        #if $index_name:
            --name "${index_name}"
        #end if
        ]]></command>
    <inputs>
        <param help="Enter a unique identifier, or leave blank to use the reference ID at end of base URL below" label="Name for this Monorail index set" name="index_name" type="text" optional="True" />
        <param label="Enter base URL for Monorail index directories (e.g. http://snaptron.cs.jhu.edu/data/monorail/ath10)" name="monorail_index_url" type="text" />
    </inputs>
    <outputs>
        <data format="data_manager_json" name="out_file" />
    </outputs>
</tool>