view data_manager/directory_data_manager.xml @ 0:d98ec2e7d569 draft

Uploaded first version

<tool id="directory_data_manager" name="directory data manager" tool_type="manage_data" version="0.0.1">
    <description>path inputer</description>
    <command interpreter="python">
        directory_data_manager.py
        --value "${value}" 
        --dbkey "${dbkey}" 
        --name "${name}" 
        --path "${path}" 
        --data_table_name "directory_data" 
        --json_output_file "${json_output_file}"
    </command>
    <inputs>
        <param name="path" type="text" value="" label="path field for the entry" />
        <param name="original_extension" type="text" value="" label="Extensions as found in directory." />
        <param name="galaxy_extension" type="text" value="" label="Galaxay Extension." />
        <param name="decompress" type="select" label="Will files need to be decompressed.">
            <option value="Yes">Yes. Files should decompressed (unzipped)</option>
            <option value="No">No. Files are not compressed</option>
        </param>
        <param name="value" type="text" value="" label="value field for the entry.  Defaults to name if left blank." />
        <param name="dbkey" type="text" value="" label="dbkey field for the entry.  Defaults to value if left blank." />
        <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." />
    </inputs>
    <outputs>
        <data name="json_output_file" format="data_manager_json"/>
    </outputs>

    <help>
Adds information for downloading data to the directory_data data table.

Reguried inputs are.

path: Full path on the server where galaxy can find the files

Original Extension: The Extention as found on the server.
    Parts before the extension that could be used to split the data into seubsection such are Read1 and Read2 should not e included.

Galaxy_Extension: The Extention to give the file before loading into galaxy so galaxy can detect the file type.
    This should be one as listed in galaxy/config/datatypes_conf.xml (or xml.sample)
    For example use tabular for tsv, txt for text and fasta and not fa
    Ideally use fastqsanger, fastqsolexa, fastqcssanger, or fastqillumina instead of just fastq as many tools need this level of detail.

Decompress: 'Yes' to ask the tool to decompress the files otherwise 'No'. Any other value will cause an error. 

If name is not provided the filename from path less the exstension is used.

If value is not provided, the name will be used (or its default)

If dbkey is not provided, the value will be used (or its default)

===

The tool will check the path exists and that it holds at least one file with the required extension.

    </help>
    <citations>
    </citations>

</tool>