<tool id="get_fasta_reference" name="get fasta reference"  version="0.3.1">
<description>Obtain reference genome sequence</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        cat "$pre_installed_fasta.fields.path" > "$output"
    ]]></command>
    <inputs>
          <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="pre_installed_fasta" type="select">
          <options from_data_table="all_fasta"/>
          </param>
    </inputs>
    <outputs>
        <data name="output" label="${pre_installed_fasta.value_label}" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="pre_installed_fasta" value="EcR_USP_224.fa"/>
            <output name="output" file="EcR_USP_224.fa"/>
        </test>
    </tests>
    <help><![CDATA[
Places the galaxy instance pre-built genome index sequence in the current history.    
Useful for sharing purposes or tools that work directly on fasta files.
    ]]></help>
    <citations>
        <citation type="doi">10.1186/gb-2010-11-8-r86</citation>
    </citations>
</tool>