<tool id="tbl2gff3" name="Table to GFF3" version="1.2">
	<description></description>
	<macros>
		<import>macros.xml</import>
	</macros>
	<expand macro="requirements"/>
	<command detect_errors="exit_code">
	<![CDATA[
		python '$__tool_directory__/tbl2gff3.py'
			'$table'
			'$rid'
			'$begin'
			'$end'

			#if $type:
				--type '$type'
			#end if

			#if $score:
				--score '$score'
			#end if

			#if $source:
				--source '$source'
			#end if

			#if str($strand.strand_select) == 'infer':
				--strand_infer
			#else if str($strand.strand_select) != "none":
				--strand_${strand.strand_select} '${strand.strand}'
			#end if

			#for $a in $attributes
				-a '${a.key}:${a.val}'
			#end for

			> '$output'
	]]></command>
	<inputs>
		<param label="Table" name="table" type="data" format="tabular"/>

		<param name="rid" type="text" value="1" label="Record ID column or value" optional="false" help="@HELP@"/>
		<param name="begin" type="text" value="" optional="false" label="Start column or value" help="@HELP@"/>
		<param name="end" type="text" value="" optional="false" label="End column or value" help="@HELP@"/>
		<param name="type" type="text" value="sequence_feature" label="Type column or value" help="@HELP@"/>
		<param name="score" type="text" value="" label="Score column or value" help="@HELP@"/>
		<param name="source" type="text" value="tbl2gff3" label="Source column or value" help="@HELP@"/>


		<conditional name="strand">
			<param name="strand_select" type="select" label="Strand">
				<option value="infer">Infer</option>
				<option value="none">Not specified</option>
				<option value="column">From Column</option>
				<option value="value">Specify Value</option>
			</param>
			<when value="none" />
			<when value="infer" />
			<when value="column" >
				<param name="strand" type="text" value="" label="Strand column" />
			</when>
			<when value="value">
				<param name="strand" type="integer" value="1" min="-1" max="1" label="Strand value" />
			</when>
		</conditional>

		<repeat name="attributes" title="Qualifiers" help="Other columns can be turned into qualifiers with arbitrary keys and values">
			<param name="key" type="text" value="key" label="Name of the qualifier"/>
			<param name="val" type="text" value="" label="Qualifier value column or raw text" help="@HELP@"/>
		</repeat>

	</inputs>
	<outputs>
		<data format="gff3" name="output"/>
	</outputs>
	<tests>
		<test>
			<param name="table" ftype="tabular" value="input.tab" />
			<param name="rid" value="1" />
			<param name="begin" value="5" />
			<param name="end" value="6" />
			<param name="score" value="14" />
			<conditional name="strand">
				<param name="strand_select" value="value"/>
				<param name="strand" value="1"/>
			</conditional>
			<repeat name="attributes">
				<param name="key" value="e-value" />
				<param name="val" value="7" />
			</repeat>
			<repeat name="attributes">
				<param name="key" value="hit" />
				<param name="val" value="9" />
			</repeat>
			<repeat name="attributes">
				<param name="key" value="GI" />
				<param name="val" value="11" />
			</repeat>
			<repeat name="attributes">
				<param name="key" value="test" />
				<param name="val" value="one" />
			</repeat>
			<repeat name="attributes">
				<param name="key" value="test" />
				<param name="val" value="two" />
			</repeat>

			<output name="output" file="blast.gff3" />

		</test>
		<test>
			<param name="table" ftype="tabular" value="infer.tab" />
			<param name="rid" value="1" />
			<param name="begin" value="2" />
			<param name="end" value="3" />
			<conditional name="strand">
				<param name="strand_select" value="infer"/>
			</conditional>
			<output name="output" file="infer.gff3" />

		</test>
	</tests>
	<help><![CDATA[
**What it does**

Convert a table into GFF3. This is not a very complex or advanced tool, it won't produce GFF with hierarchy, just flat gff3 which may be sufficient for visualisation purposes.

]]></help>
	<citations>
	</citations>
</tool>