--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml	Fri Jan 16 17:40:04 2015 -0500
@@ -0,0 +1,60 @@
+<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>