view sqlite_to_tabular.xml @ 2:bc50a7b7f246 draft

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<?xml version="1.0"?>
<tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1">
    <description>for SQL query</description>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <configfiles>
        <configfile name="query_file">
$sqlquery
        </configfile>
    </configfiles>

    <command interpreter="python">
    sqlite_to_tabular.py 
    --sqlitedb="$sqlitedb" 
    --query_file="$query_file"
    $no_header 
    --output="$query_results"
    </command>
    <inputs>
        <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
        <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
            <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator>
            <sanitizer sanitize="False"/>
        </param>
        <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/>
    </inputs>
    <outputs>
        <data name="query_results" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="sqlitedb" ftype="sqlite" value="testdb.sqlite" />
            <param name="sqlquery" value="SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'" />
            <output name="query_results">
                <assert_contents>
                    <has_text text="Smith" />
                    <not_has_text text="Doe" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        Outputs the results of a query on a SQLite Database as a tabular file. 
    </help>
</tool>