view cpt_convert_glimmer_to_gff3.xml @ 0:55414aa8c226 draft default tip

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<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.util.glimmer3_to_gff3" name="Glimmer3 to GFF3" version="19.1.0.0">
	<description>convert formats</description>
	<macros>
		<import>cpt-macros.xml</import>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
	<command detect_errors="aggressive">
@GENOME_SELECTOR_PRE@

python $__tool_directory__/cpt_convert_glimmer_to_gff3.py
$glimmer
@GENOME_SELECTOR@
> $data
</command>
	<inputs>
		<param label="Glimmer Output" name="glimmer" type="data" format="tabular,txt"/>
		<expand macro="genome_selector" />
	</inputs>
	<outputs>
		<data format="gff3" name="data">
		</data>
	</outputs>
	<tests>
		<test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="ConvGlim_In.fasta" />
			<param name="glimmer" value="ConvGlim_In.out" />
			<output name="data" file="ConvGlim_Out.gff3" />
		</test>
	</tests>
	<help>
	**What it does**

	Converts an input Glimmer3 table to the GFF3 format. If the Glimmer3 output indicates a gene wrapping 
	around over the sequence boundary (as if circular) then it will only convert the upstream fragment and 
	label it as "_truncated" in the resulting GFF.
	</help>
		<expand macro="citations" />
</tool>