<?xml version="1.0" ?>

<tool id="generate_genomeid" name='Generate GenomeID' version='1.0.0' hidden='false'>

	<command interpreter="perl">
		generateID.pl --o $genomeID --n $noise --hg $hg --b $baq --s $sex --u $ucn --r $ref 
		#if $source.source_select=="bam"
--type bam --file $bamFile
		#elif $source.source_select=="vcf"
--type vcf --file $vcfFile
		#else
--type tbi --file $tbi_gz 
		#end if
		#if $sampleName 
--sN $sampleName
		#end if

	</command>

	<inputs>
		<conditional name="source">
			<param name="source_select" type="select" label="Sequence Source Type">
				<option value="bam">Binary Alignment Map (BAM)</option>
				<option value="vcf">Variant Call Format (VCF)</option>
				<option value="tbi">Indexed TAB-delimited (TABIX)</option>
			</param>
			
			<when value="bam">
				<param name="bamFile" type="data" format="bam" label="BAM file" help="If file is not listed, ensure it is set to bam datatype"></param>
			</when>

			<when value="vcf">
				<param name="vcfFile" type="data" format="vcf" label="VCF File" help="If file is not listed, ensure it is set to vcf datatype"></param>
			</when>

			<when value="tbi">
				<param name="tbi_gz" type="data" format="vcf_bgzip" label="Compressed VCF File" help="If file is not listed, ensure it is set to vcf_bgzip datatype"></param>
			</when>

		</conditional>
			
			<param name="hg" type="select" label="Version of the reference Human Genome" help="Warning: Selection of Unknown may return a poor identifier">
				<option value="hg19">Human Genome Version 19</option>
				<option value="hg38">Human Genome Version 38</option>
				<option value="none">Unknown</option>
			</param>
			
			<param name="sampleName" type="text"  label="Name of the sample" help="Used if source file contains more than one sample"></param>
			<param name="noise" type="float" value="0.05" label="Threshold for maximum allowed noise"></param>
			<param name="baq" type="integer" value="30" label=""></param>
			<param name="sex" type="boolean" checked="true" label="Include Sex Chromosome Information"></param>
			<param name="ucn" type="boolean" checked="false" label="Sample has unusual copy number"></param>
			<param name="ref" type="boolean" checked="false" label="Match to reference geneome if marker not found"></param>

	</inputs>
	
	<outputs>
		<data name="genomeID" format="txt" label="${sampleName}_genomeID" />
	</outputs>
</tool>