view factera/factera.xml @ 18:c793d9c3f26b draft

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<tool id="factera" name="FACTERA" version="1.4.3">
	
	<description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description>

	<requirements>
		<requirement type="package" version="0.1.19">samtools</requirement>
		<requirement type="package" version="2.2.26+">blast+</requirement>
		<requirement type="package" version="310">ucsc_user_apps</requirement>
		<requirement type="package" version="5.18.1">perl</requirement>
		<requirement type="package" version="1.4.3">factera</requirement>
		<requirement type="package" version="3.0608">perl_descriptive_statistics</requirement>
		<requirement type="set_environment">FACTERA_DIR</requirement>
	</requirements> 

	<command>		
	<!-- Run commands using Galaxy perl -->
	#if $cond.additionalOpt == "no"
		perl \$FACTERA_DIR/factera-v1.4.3.pl -o -F ./ $sortedBam $exonBed $genome2Bit;
	#else
		perl \$FACTERA_DIR/factera-v1.4.3.pl -r -F $cond.r -m $cond.m -x $cond.x -s $cond.s -f $cond.f -S $cond.S 
		-k $cond.k -c $cond.c -b $cond.b -p $cond.p -a $cond.a -o ./ $sortedBam $exonBed $genome2Bit;
	#end if

	<!-- Keep only the fusion file -->
	if [ -f "*fusions.txt" ]; then cat *fusions.txt > $outfile ; else echo "No Fusions" > $outfile ; fi
	</command>
 
	<inputs>
		<param format="bam" name="sortedBam" type="data" label="Alignment in BAM format" />
		<param format="bed" name="exonBed" type="data" label="Genomic coordinates with gene/exon names in fourth column" />		
		<param format="twobit" name="genome2Bit" type="data" label="Two bit reference sequence" />	
		<conditional name="cond">	
			<param type="select" name="additionalOpt" label="Additional Options">
				<option value="yes">Yes</option>
				<option value="no" selected="True">No</option>
			</param>
			<when value="yes"> 
				<!-- Names follow command line flags in factera.pl -->
				<param type="integer" name="r" label="Minimum number of breakpoint-scanning reads required for output" value="5"/>
				<param type="integer" name="m" label="Minimum number of discordant reads required for each candidate fusion" value="2"/>
				<param type="integer" name="x" label="Maximum number of breakpoints to examine for each pair of genomic regions" value="5"/> 
				<param type="integer" name="s" label="Minimum number of reads with the same breakpoint" value="1"/>
				<param type="float" name="f" min="0" max="1" label="Minimum fraction of read bases required for alignment to fusion template" value=".9"/>
				<param type="float" name="S" min="0" max="1" label="Minimum similarity required for read to match fusion template" value=".95"/>
				<param type="integer" name="k" label="K-mer size (number of bases) for fragment comparison" value="10"/>
				<param type="integer" name="c" label="Minimum size of soft-clipped region to consider" value="16"/>
				<param type="integer" name="b" label="Number of bases flanking breakpoint for fusion template" value="500"/>
				<param type="integer" name="p" label="Number of threads for blastn search" value="4"/>
				<param type="integer" name="a" label="Number of bases flanking breakpoint to provide in output" value="50"/>
			</when>		
		</conditional>
	</inputs>	
  
	<outputs>
		<data format="tabular" name="outfile" />	
	</outputs>
  
	<help>This tool does Factera</help>

</tool>