view validate_affy_metadata.xml @ 4:9d5a14c913b1 draft

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<tool id="validate_affy_metadata" name="Validate Affymetrix metadata" version="1.0.0">
    <description>for 96 well plate</description>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/validate_affy_metadata.py'
--input '$input'
--output '$output']]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Affymetrix 96 well plate metadata file">
            <validator type="expression" message="96 well plate data must have 32 columns"><![CDATA[value is not None and value.metadata.columns==32]]></validator>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="affy_metadata.tabular" ftype="tabular"/>
            <output name="output" file="affy_metadata.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
**What it does**

Validates an Affymetrix metadata file for 96 well plate data consisting of 32 columns.
The tool will output the input file if it is valid.

-----

**Columns**

 * user_specimen_id
 * field_call
 * bcoral_genet_id
 * bsym_genet_id
 * reef
 * region
 * latitude
 * longitude
 * geographic_origin
 * colony_location
 * depth
 * disease_resist
 * bleach_resist
 * mortality
 * tle
 * spawning
 * collector_last_name
 * collector_first_name
 * org
 * collection_date
 * contact_email
 * seq_facility
 * array_version
 * public
 * public_after_date
 * sperm_motility
 * healing_time
 * dna_extraction_method
 * dna_concentration
 * registry_id
 * result_folder_name
 * plate_barcode
    </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>