<tool id="mapperAnalyzer" name="mapper analyzer">
	<description>Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. </description>
	<command interpreter="python">
		../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff3':
			-f gff3	
		#elif $formatType.FormatInputFileName1 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName1 == 'bam':
			-f bam
		#elif $formatType.FormatInputFileName1 == 'seqmap':
			-f seqmap
		#end if
			
		-q $formatType2.inputFileName2
		#if $formatType2.FormatInputFileName2 == 'fasta':
			-k fasta
		#elif $formatType2.FormatInputFileName2 == 'fastq':
			-k fastq	
		#end if
		

		#if $optionnumber.number == 'Yes':
			-n $optionnumber.numberVal
		#end if
		#if $optionsize.size == 'Yes':
			-s $optionsize.sizeVal
		#end if
		#if $optionidentity.identity == 'Yes':
			-d $optionidentity.identityVal
		#end if
		#if $optionmismatch.mismatch == 'Yes':
			-m $optionmismatch.mismatchVal
		#end if
		#if $optiongap.gap == 'Yes':
			-p $optiongap.gapVal
		#end if		
		#if $optiontitle.title == 'Yes':
			-t $optiontitle.titleVal
		#end if	
		#if $optionappend.append == 'Yes':
			-a $optionappend.appendfile
		#end if	
			
		$merge
		$remove
		$remain
		-o $outputFileGFF
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName1" type="select" label="Input File mapping Format">
				<option value="bed">bed</option>
				<option value="gff3">gff3</option>
				<option value="sam">sam</option>
				<option value="bam">bam</option>
				<option value="seqmap" selected="true">seqmap</option>
			</param>
			<when value="bed">
				<param name="inputFileName1" format="bed" type="data" label="Input File"/>
			</when>
			<when value="gff3">
				<param name="inputFileName1" format="gff3" type="data" label="Input File"/>
			</when>
			<when value="sam">
				<param name="inputFileName1" format="sam" type="data" label="Input File"/>
			</when>
			<when value="bam">
				<param name="inputFileName1" format="bam" type="data" label="Input File"/>
			</when>
			<when value="seqmap">
				<param name="inputFileName1" format="seqmap" type="data" label="Input File"/>
			</when>
		</conditional>

		<conditional name="formatType2">
			<param name="FormatInputFileName2" type="select" label="Reference sequence File Format">
				<option value="fasta" selected="true">fasta</option>
				<option value="fastq">fastq</option>
			</param>
			<when value="fasta">
				<param name="inputFileName2" format="fasta" type="data" label="Reference sequence File Format"/>
			</when>
			<when value="fastq">
				<param name="inputFileName2" format="fastq" type="data" label="Reference sequence File Format"/>
			</when>
		</conditional>


		<conditional name="optionnumber">
			<param name="number" type="select" label="max. number of occurrences of a sequence">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="numberVal" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionsize">
			<param name="size" type="select" label="minimum pourcentage of size ">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="sizeVal" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionidentity">
			<param name="identity" type="select" label="minimum pourcentage of identity ">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="identityVal" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optionmismatch">
			<param name="mismatch" type="select" label="maximum number of mismatches">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="mismatchVal" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optiongap">
			<param name="gap" type="select" label="maximum number of gaps">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="gapVal" type="integer" value="0"/>
			</when>
			<when value="No">
			</when>
		</conditional>

		<conditional name="optiontitle">
			<param name="title" type="select" label="title of the plots ">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="titleVal" type="text" value="title of the UCSC track" />
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<conditional name="optionappend">
			<param name="append" type="select" label="append to GFF3 file">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="appendfile" type="data" format="gff3" label="append a file"/>
			</when>
			<when value="No">
			</when>
		</conditional>
		
		<param name="merge" type="boolean" truevalue="-e" falsevalue="" checked="false" label="merge exons when introns are short "/>
		<param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/>
		<param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/>
	</inputs>

	<outputs>
		<data name="outputFileGFF" format="gff3" label="[mapperAnalyzer] out file"/>
	</outputs> 
	
</tool>