view pg-query.xml @ 0:fa1a61331039 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272

<tool id="pg_query" name="Query" version="@PG_VERSION@">
    <description>postgres database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
            @UNTAR_INFILE@ &&
            @PG_START@ &&
            ##ls -l ./postgresql &&
            a=" with CSV HEADER DELIMITER '	';" &&
            echo "COPY ($query) TO STDOUT"\$a | @PSQL@ -L logfile.log > '$outfile' &&
            @PG_STOP@ 
            &&
            cat logfile.log
    ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="postgresql" label="Input database" />
        <param name="query" type="text" area="True" size="5x50" label="The query to be issued to the database">
            <sanitizer invalid_char="">
                <valid initial="string.printable">
                    <remove value="&apos;" />
                </valid>
                <mapping initial="none">
                    <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
                </mapping>
            </sanitizer>
            <validator type="expression" message="Query cannot be empty">value.strip()</validator>
         </param>
    </inputs>
    <outputs>
        <data format="txt" name="outfile" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="pg_import_result1.pg.tar.bz2" ftype="postgresql" />
            <param name="query" value="select version from migrate_version" />
            <output file="pg_query_result1.txt" name="outfile" />
        </test>
        <test>
            <param name="infile" value="pg_import_result1.pg.tar.bz2" ftype="postgresql" />
            <param name="query" value="select * from galaxy_user" />
            <output file="pg_query_result2.txt" name="outfile" />
        </test>
    </tests>
    <help>
<![CDATA[

@HELP_FOOTER@

]]>
    </help>
    <expand macro="citations" />
</tool>