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<tool id="lumpy" name="LUMPY" version="0.2.9">
	<description>
		a probabilistic framework for structural variant discovery
	</description>
	<requirements>
		<requirement type="package" version="0.1.19">samtools</requirement>
		<requirement type="package" version="0.2.9">lumpy</requirement>
		<requirement type="set_environment" version="0.2.9">LUMPY_SCRIPTS</requirement>
		<requirement type="package" version="1.9">numpy</requirement>
	</requirements>
	<command>

		<!-- Create Symbolic links to bam and bam indexes -->
        ln -s $normal normal.bam;
        ln -s $normal.metadata.bam_index normal.bam.bai;
        ln -s $tumour tumour.bam;
        ln -s $tumour.metadata.bam_index tumour.bam.bai;

		<!-- EXTRACT DISCORDANT PAIRED END ALIGNMENTS -->
		samtools view -F 1294 -b normal.bam | samtools sort - normal.pe;
		samtools view -F 1294 -b tumour.bam | samtools sort - tumour.pe;

		<!-- EXTRACT SPLIT-READ ALIGNMENTS -->
		samtools view -h normal.bam |
		  \$LUMPY_SCRIPTS/extractSplitReads_BwaMem -i stdin |
		  samtools view -Sb - |
		  samtools sort - normal.sr;
		samtools view -h tumour.bam |
		  \$LUMPY_SCRIPTS/extractSplitReads_BwaMem -i stdin |
		  samtools view -Sb - |
		  samtools sort - tumour.sr;

		<!-- CREATE HISTO FILE -->
		samtools view normal.bam |
		  tail -n+100000 |
		  \$LUMPY_SCRIPTS/pairend_distro.py -r 150 -X 4 -N 10000 -o normal.pe.histo > normal.stats;
		samtools view tumour.bam |
		  tail -n+100000 |
		  \$LUMPY_SCRIPTS/pairend_distro.py -r 150 -X 4 -N 10000 -o tumour.pe.histo > tumour.stats;

		<!-- Store MEAN and STD in nice format -->
		cat -t normal.stats | sed s/\\^\\I/,/g > normal.stats.txt;
		cat -t tumour.stats | sed s/\\^\\I/,/g > tumour.stats.txt;

		<!-- RUN LUMPY -->

	  	lumpy
	  	-e
	  	-tt $advancedsettings.tt
	  	-mw $advancedsettings.mw
	  	#if $x
	  		-x $x
	  	#end if
	
		-pe
		bam_file:normal.pe.sort.bam,
		histo_file:normal.pe.histo,
		\$(cat normal.stats.txt),
		read_length:$advancedsettings.pe_read_length,
		min_non_overlap:$advancedsettings.pe_min_non_overlap,
		discordant_z:$advancedsettings.pe_discordant_z,
		back_distance:$advancedsettings.pe_back_distance,
		min_mapping_threshold:$advancedsettings.pe_min_mapping_threshold,
		weight:$advancedsettings.pe_weight,
		#if $sampleid_source.manual:
		    id:PE-$sampleid_source.idn
		#else:
		    id:PE-\$(basename $normal)
		#end if
				
		-sr
		bam_file:normal.sr.sort.bam,
		back_distance:$advancedsettings.sr_back_distance,
		min_mapping_threshold:$advancedsettings.sr_min_mapping_threshold,
		weight:$advancedsettings.sr_weight,
		min_clip:$advancedsettings.sr_min_clip,
		#if $sampleid_source.manual:
		    id:SE-$sampleid_source.idn
		#else
		    id:SE-\$(basename $normal)
		#end if
		
		-pe
		bam_file:n=tumour.pe.sort.bam,
		histo_file:tumour.pe.histo,
		\$(cat tumour.stats.txt),
		read_length:$advancedsettings.pe_read_length,
		min_non_overlap:$advancedsettings.pe_min_non_overlap,
		discordant_z:$advancedsettings.pe_discordant_z,
		back_distance:$advancedsettings.pe_back_distance,
		min_mapping_threshold:$advancedsettings.pe_min_mapping_threshold,
		weight:$advancedsettings.pe_weight,
		#if $sampleid_source.manual:
		    id:PE-$sampleid_source.idt
		#else:
		    id:PE-\$(basename $tumour)
		#end if
				
		-sr
		bam_file:tumour.sr.sort.bam,
		back_distance:$advancedsettings.sr_back_distance,
		min_mapping_threshold:$advancedsettings.sr_min_mapping_threshold,
		weight:$advancedsettings.sr_weight,
		min_clip:$advancedsettings.sr_min_clip,
		#if $sampleid_source.manual:
		    id:SE-$sampleid_source.idt
		#else
		    id:SE-\$(basename $tumour)
		#end if

		> $outfile;

	</command>
	<inputs>
        <conditional name="sampleid_source">
            <param label="Choose the source to fetch Sample Identifiers" name="sampleid_selector" type="select">
                <option value="bamfile">BAM File Name</option>
                <option value="manual">Manual</option>
            </param>
            <when value="manual">
                <param name="idn" type="text" label="Tumour ID (Name)"/>
                <param name="idt" type="text" label="Normal ID (Name)"/>
            </when>
        </conditional>
        <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
        <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
        <param type="data" format="bed" name="x" label="Exluded Regions BED file" optional="true"/>
        <section name="advancedsettings" title="Advanced Settings" expanded="false">
    		<param type="integer" value="5" name="mw" label="Minimum Weight for Call"/>
    		<param type="integer" value="3" name="tt" label="Trim Threshold"/>
		    <param type="integer" name="pe_back_distance" value="20" label="Paired End Back Distance" help="Distance into the read to add the breakpoint interval"/>
		    <param type="integer" name="pe_min_mapping_threshold" value="1" label="Paired End Min Mapping Threshold" help="Minimum mapping quality that a read must have to be considered"/>
		    <param type="integer" name="pe_weight" value="1" label="Paired End Weight" help="Weight of each piece of evidence from this sample"/>
		    <param type="integer" name="pe_discordant_z" value="4" label="Paired End Discordant Value" help="Number of standard deviations away from the mean to be considered as a normal library size"/>
		    <param type="integer" name="pe_read_length" value="150" label="Paired End Read Length" help="Length of sequenced reads"/>
			<param type="integer" name="pe_min_non_overlap" value="150" label="Paired End Min Non Overlap" help="Number of base pair positions that must be unique to each end of a read pair"/>
			<param type="integer" name="sr_back_distance" value="20" label="Split Read Back Distance" help="Distance into the read to add the breakpoint interval"/>
			<param type="integer" name="sr_min_mapping_threshold" value="1" label="Split Read Min Mapping Threshold" help="Minimum mapping quality that a read must have to be considered"/>
			<param type="integer" name="sr_weight" value="1" label="Split Read Weight" help="Weight of each piece of evidence from this sample"/>
			<param type="integer" name="sr_min_clip" value="1" label="Spliy Read Min Clip" help="Minimum number of clipped bases to consider in a split read"/>
		</section>
	</inputs>
	<outputs>
		<data type="vcf" name="outfile"/>
	</outputs>
</tool>