--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbl2gff3.xml	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,117 @@
+<tool id="tbl2gff3" name="Table to GFF3" version="1.1">
+	<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($strand.strand_select) != "none":
+				--strand_${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="Feature start column or value" help="@HELP@"/>
+		<param name="end" type="text" value="" optional="false" label="Feature end column or value" help="@HELP@"/>
+		<param name="type" type="text" value="sequence_feature" label="Feature type column or value" help="@HELP@"/>
+		<param name="score" type="text" value="" label="Feature score column or value" help="@HELP@"/>
+		<param name="source" type="text" value="tbl2gff3" label="Feature source column or value" help="@HELP@"/>
+
+
+		<conditional name="strand">
+			<param name="strand_select" type="select" label="Strand">
+				<option value="none">Not specified</option>
+				<option value="column">From Column</option>
+				<option value="value">Specify Value</option>
+			</param>
+			<when value="none" />
+			<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>
+	</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>
+