changeset 4:bcee925a2db9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/factera.xml	Thu Jan 15 20:17:00 2015 -0500
@@ -0,0 +1,54 @@
+<tool id="factera" name="FACTERA">
+	
+	<description>Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm</description>
+
+	<command>
+		
+	<!-- Run commands using Galaxy perl -->
+	#if $cond.additionalOpt.value == "no"
+		perl $FACTERA_DIR/factera-v1.4.3.pl -o ./ $sortedBam $exonBed $genome2Bit
+	#else
+		perl $FACTERA_DIR/factera-v1.4.3.pl -r $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 -->
+	cat *fusions.txt > $outfile;
+
+	</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="2bit" 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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml	Thu Jan 15 20:17:00 2015 -0500
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  
+	<package name="blast_plus_blast_plus_2_2_26" version="2.2.26">
+    <repository changeset_revision="85e43fb3f363" name="package_blast_plus_2_2_26" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+
+	<package name="package_samtools_0_1_19" version="0.1.19">
+		<repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+	</package>
+
+	<package name="ucsc_user_apps" version="1.0.0">		
+		<repository changeset_revision="7d36c043e340" name="ucsc_user_apps" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
+	</package>
+
+	<package name="factera_perl_dependency" version="1.4.3">
+		<install version="1.0">
+			<actions>
+
+				<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz</action>
+				<action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR</action>
+				<action type="shell_command">make</action>
+				<action type="shell_command">make install</action>
+				
+				<action type="set_environment">
+					<environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/site_perl</environment_variable>
+				</action>
+
+			</actions>
+		</install>	
+	</package>
+
+	<package name="package_factera_1_4_3" version="1.4.3">
+		<install version="1.0">
+  		<actions>
+				
+      	<action type="download_by_url">http://factera.stanford.edu/files/factera-v1.4.3.pl</action>
+        
+				<action type="move_directory_files">
+					<source_directory>.</source_directory>
+					<destination_directory>$INSTALL_DIR</destination_directory>
+				</action>
+
+				<action type="set_environment">
+					<environment_variable action="set_to" name="FACTERA_DIR">$INSTALL_DIR</environment_variable>
+				</action>
+
+			</actions>
+		</install>
+	</package>
+
+</tool_dependency>