# HG changeset patch
# User malbuquerque
# Date 1421450015 18000
# Node ID da6b7323eb05378a0100ab4c531425efe39699f8
# Parent  b3103a385969d5a22664147827dc0c3ca9b537f3
Uploaded

diff -r b3103a385969 -r da6b7323eb05 factera/factera.xml
--- a/factera/factera.xml	Fri Jan 16 18:08:08 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<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 -F -o ./ $sortedBam $exonBed $genome2Bit > $outfile;
-	#else
-		perl \$FACTERA_DIR/factera-v1.4.3.pl -F -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 > $outfile;
-	#end if
-
-	<!-- Keep only the fusion file -->
-	if [ -e *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>
diff -r b3103a385969 -r da6b7323eb05 factera/tool_dependencies.xml
--- a/factera/tool_dependencies.xml	Fri Jan 16 18:08:08 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  
-	<package name="blast+" 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="samtools" 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="310">		
-		<repository changeset_revision="f945f71702cc" name="package_ucsc_user_apps_310" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
-	</package>
-
-	<package name="perl_descriptive_statistics" version="3.0608">
-		<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">$INSTALL_DIR/lib/perl5/site_perl</environment_variable>
-				</action>
-			</actions>
-		</install>	
-	</package>
-
-	<package name="factera" version="1.4.3">
-		<install version="1.0">
-  		<actions>
-      	<action type="download_by_url">http://factera.stanford.edu/files/factera-v1.4.3.pl</action>      
-				<action type="move_directory_files">
-					<source_directory>.</source_directory>
-					<destination_directory>$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>