annotate data_manager/add_ctat_centrifuge_index.xml @ 0:b4d4f0d76e94 draft default tip

Uploaded

<tool id="ctat_centrifuge_indexes_data_manager" 
    name="CTAT Centrifuge Indexes Data Manager" 
    version="1.0.0" tool_type="manage_data">
    <description>Retrieve, and/or specify the location of, a CTAT Centrifuge Index. 
    </description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <command detect_errors="default">
        <![CDATA[
        python $__tool_directory__/add_ctat_centrifuge_index.py 
            --display_name "${display_name}" 
            --destination_path "${destination}" 
            --output_filename "${out_file}" 
            #if str( $download_question.download ) == "true":
                --download_location "\"${download_question.filename}\"" 
                #if str( $download_question.force_download ) == "true":
                    --force_download 
                #end if
            #end if
        ]]>
    </command>
    <inputs>
        <!-- The following are left in here, just as examples of various ways of doing options.
            <param name="force_download" type="boolean" checked="false"
                truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" />
            <param name="download" type="select" label="Need to Download?">
                <option value="single" selected="true">Single Dataset</option>
                <option value="paired_collection">Paired Collection</option>
            <when value="paired_collection">
                 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
            </when>
        -->
        <conditional name="download_question">
            <param name="download" type="boolean" checked="false" label="Need to Download?" />
            <when value="true">
                <!-- The use of a code block to get dynamic options is now deprecated and discouraged.
                     I am still using it here. The only other way I can think of to do this is to
                     create another data_manager that gets the list of files and puts them into a
                     data_table, that is then used to get the filenames. That would require the admin
                     to first run the data_manager that builds the filename data_table before running
                     this data_manager.
                     However, I have not been able to figure out how to send information back correctly
                     from the function and there is no documentation that I have found showing how to do it.
                <param name="filename" type="select" label="Select File" display="radio" 
                    dynamic_options="get_ctat_centrifuge_index_locations()" 
                    help="Select a Centrifuge Index to Download." />
                Hard coded version.
                <param name="filename" type="text" value="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz">
                    <option value="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz">
                        p_compressed+h+v
                    </option>
                </param>
                -->
                <param name="filename" type="select" label="Select File"
                    dynamic_options="get_ctat_centrifuge_index_locations()" 
                    help="Select a Centrifuge Index to Download." />
                <param name="force_download" type="boolean" checked="false" label="Force New Download?" />
            </when>
        </conditional>

        <param name="display_name" type="text" label="Centrifuge Index Display Name" />
        <param name="destination" type="text" label="Local Destination (full path)" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
.. class:: infomark
	
Retrieve, and/or specify the location of, a CTAT Centrifuge Index.
When download is true, Centrifuge index on this FTP link_ will be downloaded.

Currently that is the only supported index.

.. class:: infomark

Specify the Full Path of the destination where the CTAT Reference Library should be placed.
If you already have the index, specify the full path of the location where it exists and leave the download box unchecked.

.. class:: infomark
 
The display_name may be left empty if downloading. 
The display_name will be used as the selector text of the entry in the data table.

.. _link: ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
    </help>
    <code file="add_ctat_centrifuge_index.py" />
</tool>