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planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/delly commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

<tool id="delly" name="DELLY" version="0.6.1">

        <description>structural variant discovery by integrated paired-end and split-read analysis</description>
	
	<macros>
		<import>citations.xml</import>
	</macros>

	<requirements>
		<requirement type="package" version="1.55.0">boost</requirement>
		<requirement type="package" version="0.6.1">delly</requirement>
		<requirement type="set_environment">DELLY_DIR</requirement>
		<requirement type="set_environment">BOOST_ROOT_DIR"</requirement>
		<requirement type="set_environment">LD_LIBRARY_PATH"</requirement>
		<requirement type="set_environment">LIBRARY_PATH"</requirement>
		<requirement type="set_environment">CPLUS_INCLUDE_PATH"</requirement>
		<requirement type="set_environment">C_INCLUDE_PATH"</requirement>
	</requirements>

	<command detect_errors="aggressive"> 

		<!-- BAM and BAI linking, (1) link BAM to new BAM file & (2) link BAM metadata to new BAI file -->
		#for $i, $s in enumerate( $repeatBam )
			ln -s $s.sortedBam ./input$(i).bam;
			ln -s $s.sortedBam.metadata.bam_index ./input$(i).bam.bai;
		#end for		

		<!-- Sets args to a list of types selected -->
		#if not isinstance( $variant_source_selector_param.value, list ):
			#set $args = [ $variant_source_selector_param.value ]
		#else:
			#set $args = $variant_source_selector_param.value
		#end if

		<!-- Run Delly Jobs for each type selected -->
		#for $option in $args
			\$DELLY_DIR/src/delly 
			  -t $option 
			  -o ./output.$(option).vcf 
			  -q $advancedsettings.mapQual 
			  -s $advancedsettings.madCutoff 
			
			#if $option == "DEL":
			  -m $advancedsettings.minFlank 
			#end if 
			
			-u $advancedsettings.genoQual 

			#if $advancedsettings.vcfgeno
			  -v $advancedsettings.vcfgeno
			#end if
                        
			#if $reference_source.reference_source_selector_param == "cached":
				-g "${reference_source.reference.fields.path}"
			#else:
				-g $reference_source.reference
			#end if

			<!-- add each input bam to command -->
			#for $i, $s in enumerate( $repeatBam ):
				./input$(i).bam	
			#end for
			;
  		#end for

		<!-- Combine VCF Files and Sort Lexographically -->
		#set $option = $args[0]
		grep ^\# output.$(option).vcf > $outfile;
		grep ^\# -v output.$(option).vcf > variants.txt;
		
		<!-- If we called more than a single variant type, concatenate all the other types variant output -->
		#if isinstance( $variant_source_selector_param.value, list ):
			#for $option in $args[1:]
				grep ^\# -v output.$(option).vcf >> variants.txt;
			#end for
		#end if
		
		<!-- Sort all variant output, assuming that it will sort lexographically by chromosome, then position, ID  -->
		<!-- In future, maybe develop a script to sort by bam header -->
		sort -k1,1d -k2,2n -k3,3d variants.txt > sortedVariants.txt;
		
		<!-- Filter Variants that have Passed Quality Checks -->
		#if $filterCalls
			awk '{if ($7 == "PASS") print $0;}' sortedVariants.txt >> $outfile;
		#else
			cat sortedVariants.txt >> $outfile;
		#end if
		
	</command>
 
	<inputs>

		<!-- REFERENCE OPTIONS -->
		<conditional name="reference_source">
			<param type="select" name="reference_source_selector_param" label="Choose the source for the reference genome">
				<option value="cached" selected="True">Use a built-in genome</option>
				<option value="history">Use a genome from the history</option>
			</param> 
			<when value="cached">
				<param type="select" name="reference" label="Genome">
					<options from_data_table="all_fasta"/>
				</param>
			</when>
			<when value="history">
				<param type="data" format="fasta" name="reference" label="Genome"/>
			</when>
		</conditional>

		<!-- VARIANT OPTIONS -->
		<param type="select" multiple="True" name="variant_source_selector_param" label="Select variants to identify in samples">
			<option value="DEL" selected="true">Deletions</option>
			<option value="DUP">Duplications</option>
			<option value="INV">Inversions</option>
			<option value="TRA">Translocations</option>
		</param>
                <!--
		<param name="interval_file" type="data" format="txt" optional="true" label="Interval file" help="Created by make parallel, only use when parallelism is turned on, note interchromosomal and intrachromosomal events have different interval files"/>
		-->
		<repeat name="repeatBam" title="Bam Alignment" min="1" default="1" >	
			<param format="bam" name="sortedBam" type="data" label="File" />		
		</repeat>
		<!-- <param name="excludeFile" type="data" format="bed" optional="true" label="Chromosomes to Exclude"/> -->
		<param name="filterCalls" type="boolean" value="false" label="Filter Poor Variant Calls"/>
		
                <section name="advancedsettings" title="Advanced Settings" expanded="false">
		<!-- Paired End Options -->
		<param name="mapQual" type="integer" value="0" min="0" max="255" label="PE - Minimum Mapping Quality" />
		<param name="madCutoff" type="integer" value="9" min="0" max="255" label="PE - Insert Size Cutoff" />

		<!-- SR Options -->
		<param name="minFlank" type="integer" value="13" label="SR - Minimum Flanking Sequence" />

		<!-- Genotyping Options -->
		<param format="vcf" name="vcfgeno" type="data" optional="true" label="GT - Input VCF" />
		<param name="genoQual" type="integer" value="20" min="0" max="255" label="GT - Minimum Mapping Quality" />
                </section>
	</inputs>
  
	<outputs>
		<data format="vcf" name="outfile" />
	</outputs>
	
	<citations>
		<expand macro="morinlab_citation"/>
		<expand macro="galaxy_citation"/>
		<expand macro="delly_citation"/>
	</citations>
  
</tool>