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<tool id="bridger" name="bridger" version="v1">
	<description>de novo assembly of RNA-Seq data</description>
	<requirements>
	<container type="docker">ycogne/bridger</container>
  </requirements>
	<command>
	   /usr/bin/Bridger_r2014-12-01/Bridger.pl 
	  
		#if $inputs.paired_or_single == "paired":

			--left $inputs.left_input

			--right $inputs.right_input

			#if $inputs.left_input.is_of_type('fasta'):
				--seqType fa
			#else:
				--seqType fq
			#end if

			#if $inputs.strand.is_strand_specific:
				--SS_lib_type $inputs.strand.library_type
			#end if

			

		#else:
			--single $inputs.input

			#if $inputs.input.is_of_type('fasta'):
				--seqType fa
			#else:
				--seqType fq
			#end if

			#if $inputs.strand.is_strand_specific:
				--SS_lib_type $inputs.strand.library_type
			#end if
		#end if

		--CPU $additional_params.CPU_usage
		-k $additional_params.kmer_used 
	   
	   -o /home/results/Bridger	2>1 ;
	   mv /home/results/Bridger/Bridger.fasta $assembled_transcripts

	   

	</command>
	 <inputs>
	  <conditional name="inputs">
			<param name="paired_or_single" type="select" label="Paired or Single-end data?">
				<option value="paired">Paired</option>
				<option value="single">Single</option>
			</param>
			<when value="paired">
				<param format="fasta,fastqsanger,fastq" argument="--left" name="left_input"  type="data" label="Left/Forward strand reads" help=""/>
				<param format="fasta,fastqsanger,fastq" argument="--right" name="right_input"  type="data" label="Right/Reverse strand reads" help=""/>
				<conditional name="strand">
					<param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
					<when value="false">
					</when>
					<when value="true">
						<param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
							<option value="FR">Forward-Reverse</option>
							<option value="RF">Reverse-Forward</option>
						</param>
					</when>
				</conditional>
			 </when>
			<when value="single">
				<param format="fasta,fastqsanger,fastq" name="input" argument="--single"  type="data" label="Single-end reads" help=""/>
				<conditional name="strand">
					<param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
					<when value="false">
					</when>
					<when value="true">
						<param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
							<option value="F">F</option>
							<option value="R">R</option>
						</param>
					</when>
				</conditional>
			</when>
		</conditional>
	 
	  <section name="additional_params" title="Additional Options" expanded="False">
					<param name="CPU_usage" argument="--CPU_usage" type="integer" optional="true" value="3" min="1" label="Number of CPU" help="Number of CPU use by the software"/>
					<param name="kmer_used" argument="-k" type="integer" optional="true" value="25" min="10" label="Kmer length" help="Kmer length"/>

		</section>
	 
		</inputs>
	<outputs>
	
		  <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" />
	 
	</outputs>
	<help>
	  https://github.com/fmaguire/Bridger_Assembler
	</help>

	
</tool>