<tool id="samifier" name="Samifier" version="1.0.8">
        <description>Samifier</description>
        <command interpreter="bash">
        samifier.sh samifier.jar $chromosome_tar -g "$genome" -m "$mapping" -o "$output1" -r "$mascot"
	#if $score_thresold
	-s "$score_thresold"
	#end if
	#if $condition2.tool_option2 == "yes"
	-l "$output2"
	#end if
	#if $condition3.tool_option3 == "yes"
	-b "$output3"
	#end if
        </command>
        <inputs>
        	<param name="chromosome_tar" type="data" format="tar" label="Select chromosome zip files" help="A zip file containing all the chromosome files" />
        	<param name="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
        	<param name="mascot" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
        	<param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
		<param name="score_thresold"  type="integer" label="Confidence Score thresold" help="Minimum confidence score for peptides to" optional="true"/>

		<conditional name="condition2">
			<param name="tool_option2" type="select" label="Write log file" help="Create an output containing the logs">
				<option value="yes" selected="No">Yes</option>
				<option value="no" selected="Yes">No</option>
			</param>
		</conditional>
		<conditional name="condition3">
			<param name="tool_option3" type="select" label="Write output in bed format" help="Output to write IGV regions of interest">
				<option value="yes" selected="No">Yes</option>
				<option value="no" selected="Yes">No</option>
        		</param>
        	</conditional>
        </inputs>
        <outputs>
                <data format="sam" name="output1" />
                <data format="txt" name="output2" label="Samifier log file">
                	<filter>condition2['tool_option2'] == "yes"</filter>
                </data>
                <data format="bed" name="output3" label="Samifier Bed">
                	<filter>condition3['tool_option3'] == "yes"</filter>
                </data>
        </outputs>
        <help>
        </help>
</tool>