annotate sqlite_to_tabular.xml @ 0:859064f07be4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d

<?xml version="1.0"?>
<tool id="sqlite_to_tabular" name="SQLite to tabular" version="1.0.0">
    <description>for SQL query</description>

    <macros>
         <import>macros.xml</import>
    </macros>

    <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/sqlite_to_tabular.py'
    --sqlitedb='$sqlitedb' 
    --query_file='$query_file'
    $no_header 
    --output='$query_results'
    ]]></command>
    <configfiles>
        <configfile name="query_file">
$sqlquery
        </configfile>
    </configfiles>
    <inputs>
        <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
        <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
            <validator type="regex">(?ims)^\s*SELECT\s.*\sFROM\s.*$</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><![CDATA[
=================
SQLite to Tabular
=================

**Inputs**

  An existing SQLite_ data base.


**Outputs**

  The results of a SQL query are output to the history as a tabular file.



@QUERY_HELP@

    ]]></help>
</tool>