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<tool id="TransTermHP" name="TransTermHP" version="19.1.0.0">
	<description>predicts transcription terminators</description>
	<macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
	</macros>
        <requirements>
		<requirement type="package" version="3.7.9">python</requirement>
		<requirement type="package" version="1.77">biopython</requirement>
	        <requirement type="package" version="2.09">transtermhp</requirement> 
                <requirement type="package" version="1.1.3">cpt_gffparser</requirement> 
                <requirement type="package" version="1.5">bcftools</requirement>   
        </requirements>
	<command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

$__tool_directory__/transterm.py
@GENOME_SELECTOR@
$gff3_data

> $output

]]>
	</command>
	<inputs>
		<expand macro="genome_selector" />
		<expand macro="gff3_input" />
	</inputs>
	<outputs>
		<data name="output" label="Terminators from ${gff3_data.name}" format="gff3" />
	</outputs>
	<tests>
		<test>
			<param name="genome_fasta" value="Transterm_In.fa" />
			<param name="gff3_data" value="Transterm_In.gff3" />
			<output name="output" file="Transterm_Out.gff3" />
		</test>
	</tests>
	<help>
*TransTermHP* finds rho-independent transcription terminators in bacterial
genomes. Each terminator found by the program is assigned a confidence
value that estimates its probability of being a true terminator.
	</help>
	<citations>
		<citation type="doi">10.1186/gb-2007-8-2-r22</citation>
	</citations>
</tool>