view update_stag_database.xml @ 0:572cf766c59d draft

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<tool id="update_stag_database" name="Update stag database" version="1.0.0">
    <description>with new genotyped samples</description>
    <command detect_errors="exit_code"><![CDATA[
#set input_dir = "input_dir"
mkdir $input_dir &&
#for $i in $input:
    #set filename = $i.file_name
    #set name = $i.name
    ln -s $filename $input_dir/$name &&
#end for
python '$__tool_directory__/update_stag_database.py'
--config_file $__tool_directory__/usd_config.ini
--database_connection_string '$__app__.config.corals_database_connection'
--input_dir '$input_dir'
--output '$output']]></command>
    <inputs>
        <param name="input" format="tabular" type="data_collection" collection_type="list" label="Tabular datasets for database update"/>
    </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**

Accepts a set of tabular datasets, one for each appropriate table in the corals (stag) database, and
updates the table with the data.  The database must be Postgres, and this tool exports the database
into a file stored in a specified directory on disk before the database is updated.
    </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>