view export_all_sample_data.xml @ 1:633cb7831526 draft

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<tool id="export_all_sample_data" name="Export all sample data" version="1.0.0">
    <description>from the stag database</description>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/export_all_sample_data.py'
--database_connection_string '$__app__.config.corals_database_connection'
--output '$output']]></command>
    <inputs>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name}"/>
    </outputs>
    <tests>
        <test>
            <!--Testing this tool is a bit difficult at the current time.-->
        </test>
    </tests>
    <help>
**What it does**

Generates a tabular dataset of all samples and associated metadata in the stag database.

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**Output Columns**

 * Affymetrix ID
 * Sample ID
 * User Specimen ID
 * Field Call
 * Sample Depth
 * Percent Missing Data Coral
 * Percent Heterozygous Coral
 * Percent Acerv Coral
 * Percent Apalm Coral
 * Bcoral Genet ID
 * Registry ID
 * DNA Extraction Method
 * DNA Concentration
 * Colony Location
 * Colony Latitude
 * Colony Longitude
 * Colony Depth
 * Reef Name
 * Region
 * Reef Latitude
 * Reef Longitude
 * GPS Coordinates Associated With
 * Coral MLG Clonal ID
 * Coral MLG Rep Sample ID
 * Genetic Coral Species Call
 * Spawning
 * Sperm Motility
 * TLE
 * Disease Resist
 * Bleach Resist
 * Mortality
 * Healing Time
 * Sequencing Facility
 * Array Version
 * Plate Barcode
 * Collector Last Name
 * First Name
 * Organization
 * Email
 * Collection Date
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {Baums I},
            title = {Manuscript in preparation},
            year = {None},
            url = {http://baumslab.org}
        </citation>
    </citations>
</tool>