<tool id="protgenerator" name="Protein Generator" version="1.0.8">
        <description>Protein Generator</description>
        <command interpreter="bash">
       	protein_generator.sh protein_generator.jar 
        -d "$databasename" 
        -f "$genomeFile" 
        #if $GlimmerFile
        	-g "$GlimmerFile"
        #end if
        #if $SplitInterval
        	-i "$SplitInterval"
        #end if
        	-o "$output1"
        #if $condition1.gffFile == "yes"
		-p "$output2"
	#end if
	#if $condition2.accessionFile == "yes"
		-q "$output3"
	#end if
	#if $trans_tab_file
		-t "$trans_tab_file"
	#end if
        </command>
        <inputs>
        	<param name="databasename" type="text" label="Database name" />
        	<param name="genomeFile" type="data" format="faa" label="Select genome file" help="Genome file in gff format" />

        	<param name="GlimmerFile" type="data" format="txt" label="Select Glimmer File" help="Glimmer txt file. Can't be used with the Split Interval" optional="true" />
		<param name="SplitInterval" type="integer" label="Size of the intervals" help="Size of the intervals (number of codons) into which the genome will be split. Can't be used with the Glimmer File" optional="true" />

		<param name="trans_tab_file" type="data" format="txt" label="Select Translation Table File" help="File containing a mapping of codons to amino acids, in the format used by NCBI." optional="true" />
		<conditional name="condition1">
			<param name="gffFile" type="select" help="write the GFF file">
				<option value="yes" selected="True">Yes</option>
				<option value="no" selected="False">No</option>
			</param>
		</conditional>
		<conditional name="condition2">
			<param name="accessionFile" type="select" label="Accession File" help="Write the accession file">
				<option value="yes" selected="True">Yes</option>
				<option value="no" selected="False">No</option>
			</param>
		</conditional>
	</inputs>
        <outputs>
                <data format="sam" name="output1" />
		<data format="gff" name="output2" label="GFF file">
			<filter>condition1['gffFile'] == "yes"</filter>
		</data>
                <data format="txt" name="output3" label="Accession File">
                	<filter>condition2['accessionFile'] == "yes"</filter>
                </data>
        </outputs>
        <help>
        </help>
</tool>