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<tool id="alignreads" name="alignReads" version="0.0.1">

    <description>alignReads: short read alignment tool wrapper</description>
    <requirements>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command interpreter="python">

        trinityToolWrapper.py util/alignReads.pl --target $target -o alignment --aligner $aligner_selection.aligner


        ## Inputs.
        #if str($inputs.paired_or_single) == "paired":
            --left $inputs.left_input --right $inputs.right_input
            #if  $inputs.left_input.ext == 'fa':
                --seqType fa
            #else:
                --seqType fq
            #end if
            #if str($inputs.library_type) != "None":
                --SS_lib_type $inputs.library_type
            #end if
			--max_dist_between_pairs $inputs.max_dist_between_pairs
        #else:
            --single $inputs.input
            #if  str($inputs.input.ext) == 'fa':
                --seqType fa
            #else:
                --seqType fq
            #end if
            #if str($inputs.library_type) != "None":
                --SS_lib_type $inputs.library_type
            #end if
        #end if

        ## Additional parameters.
	    ##if str($inputs.use_additional) == "yes":
		##	-- $inputs.additional_params
        ##end if
	
                
        ## direct to output
	    > outCapture.txt  


    </command>
    <inputs>
		<param format="fasta" name="target" type="data" label="target" help="Fasta sequences targeted for short-read alignment"  />

        <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,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
                <param name="library_type" type="select" label="Strand-specific Library Type">
                    <option value="None">None</option>
                    <option value="FR">FR</option>
                    <option value="RF">RF</option>
                </param>
                <param name="max_dist_between_pairs" type="integer" value="2000" min="1" label="max_dist_between_pairs" help="Maximum length expected between fragment pairs as aligned to the target, including introns where relevant."/>


            </when>
            <when value="single">
                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
                <param name="library_type" type="select" label="Strand-specific Library Type">
                    <option value="None">None</option>
                    <option value="F">F</option>
                    <option value="R">R</option>
                </param>
            </when>
        </conditional>

		<conditional name="aligner_selection">
			<param name="aligner" type="select" label="Select alignment tool to run">
				<option value="bowtie">bowtie</option>
				<option value="bwa">bwa</option>
				<option value="blat">blat</option>
			</param>
			<when value="blat">
				<param name="max_intron_length" type="integer" value="10000" min = "1" label="maximum intron length" help="" />
				<param name="min_percent_identity" type="integer" value="95" min="1" label="minimum percent identity" help="" />
			</when>
			<when value="bwa">
			</when>
			<when value="bowtie">
			</when>
		</conditional>


	<!--	    	
		<conditional name="use_additional_params">
            <param name="use_additional" type="select" label="Use Additional Params?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">            
				<param name="additional_params" type="text" value="" label="Additional command-line parameters to aligner" help="" />
            </when>
        </conditional>
    
	-->

    </inputs>
    <outputs>
        <data format="bam" name="coordSortedBam" label="${tool.name} on ${on_string}: COORD-sorted read alignments" from_work_dir="alignment/alignment.coordSorted.bam"/>
		<data format="bam" name="nameSortedBam" label="${tool.name} on ${on_string}: NAME-sorted read alignments" from_work_dir="alignment/alignment.nameSorted.bam"/>

		<!-- notes: need to retain:
			 -the sample name for the alignment
			 -coordinate-sorted vs. name-sorted bam file
			 -paired vs. unpaired vs. strictly proper pairs (for RSEM)
			 -strand-specific or not
		-->

	</outputs>
    <tests>


		<test>
			<param name="target" value="trinity/Trinity.fasta" />
			<param name="aligner" value="bowtie" />
			<param name="paired_or_single" value="single" />
			<param name="library_type" value="None" />
			<param name="input" value="trinity/reads.left.fq" />
        </test>
	

    </tests>
    <help>
        .. _Trinity: http://trinityrnaseq.sourceforge.net
    </help>
</tool>