<tool id="ensure_synced" name="Ensure synchronized" version="1.0.0">
    <description>analysis components</description>
    <command detect_errors="exit_code"><![CDATA[
#set affy_ids_from_file = 'affy_ids_from_file.txt'
grep "#CHROM" $input > test.head &&
tr '\t' '\n' < test.head > $affy_ids_from_file &&
python '$__tool_directory__/ensure_synced.py'
--database_connection_string '$__app__.config.corals_database_connection'
--affy_ids_from_file '$affy_ids_from_file'
--output '$output']]></command>
    <inputs>
        <param name="input" format="vcf" type="data" label="All genotyped samples file"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} (process log) on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <!--Testing this tool is a bit difficult at the current time.-->
        </test>
    </tests>
    <help>
**What it does**

Compares the set of Affymetrix id strings contained within a selected VCF file with the set of Affymetrix ids contained
in the affy_id column of the sample table in the corals (stag) database for all samples not in a failed state.  If these
sets are equivalent, the file and the database are considered to be in sync with each other.
    </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>