<tool id="bowtiebuild" name="Bowtie Indexing">
	<description>Build index for Bowtie alignment</description>

	<requirements>
                <requirement type="perl-module">bowtie_build_wrapper.pl</requirement>
        </requirements>

        <command interpreter="perl">
		./bowtie_build_wrapper.pl $fastafile "$output.files_path" $output "$fastafile.name"
	</command>

	<inputs>
		<param format="fasta" name="fastafile" type="data" optional="false" label="Fasta reference file" help="Reference file in fasta format"/>
	</inputs>

	<outputs>
		<data format="bowtie_html_index" name="output"/>
	</outputs>

	<help>
	</help>
</tool>