<tool id="glimmer2gff" name="Convert Glimmer to GFF" version="0.1">
	<description>Converts Glimmer Files to GFF Files</description>
	<command interpreter="python">glimmer2gff.py $input > $output</command>
	<inputs>
		<param name="input" type="data" format="tabular" label="Glimmer Output File"/>
	</inputs>
	<outputs>
		<data name="output" type="data" format="gff"/>
	</outputs>
	<tests>
		<test>

		</test>
	</tests>
	<help>

**What it does**

Converts a Glimmer3 output File to an GFF Annotation File::

**Example**

Input::
    >contig00097 sbe.0.234 
    orf00003     2869      497  -2     5.60
    orf00005     3894     2875  -1     7.05
    orf00007     4242     4826  +3     8.04
    orf00010     4846     5403  +1     8.57
    orf00012     6858     5413  -1    10.87
    orf00013     6857     7594  +2     3.61
    orf00014     7751     9232  +2    11.34
    orf00015     9374    10357  +2    10.66
    orf00017    10603    11196  +1    13.39
    orf00021    11303    11911  +2     8.81
    orf00025    14791    12050  -2    13.51
    orf00026    15216    16199  +3     6.37
    orf00028    16333    16935  +1     8.86


Output:
    contig00097 sbe.0.234	glimmer	gene	497	2869	.	-	.	-2     5.60
    contig00097 sbe.0.234	glimmer	gene	2875	3894	.	-	.	-1     7.05
    contig00097 sbe.0.234	glimmer	gene	4242	4826	.	+	.	+3     8.04
    contig00097 sbe.0.234	glimmer	gene	4846	5403	.	+	.	+1     8.57
    contig00097 sbe.0.234	glimmer	gene	5413	6858	.	-	.	-1    10.87
    contig00097 sbe.0.234	glimmer	gene	6857	7594	.	+	.	+2     3.61
    contig00097 sbe.0.234	glimmer	gene	7751	9232	.	+	.	+2    11.34
    contig00097 sbe.0.234	glimmer	gene	9374	10357	.	+	.	+2    10.66
    contig00097 sbe.0.234	glimmer	gene	10603	11196	.	+	.	+1    13.39
    contig00097 sbe.0.234	glimmer	gene	11303	11911	.	+	.	+2     8.81
    contig00097 sbe.0.234	glimmer	gene	12050	14791	.	-	.	-2    13.51
    contig00097 sbe.0.234	glimmer	gene	15216	16199	.	+	.	+3     6.37
    contig00097 sbe.0.234	glimmer	gene	16333	16935	.	+	.	+1     8.86


-----	


	</help>
</tool>