# HG changeset patch
# User yhoogstrate
# Date 1427976364 14400
# Node ID f06461883f7b67fa78893b16ce5f9202ced71438
# Parent  76293f7745ff4652df38c3837d10bf4cf1614979
updated to version 2.7.1 and extended wrapper with additional output type and a help section

diff -r 76293f7745ff -r f06461883f7b fuma.xml
--- a/fuma.xml	Sun Mar 29 05:28:17 2015 -0400
+++ b/fuma.xml	Thu Apr 02 08:06:04 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="fuma" name="FuMa" version="2.6.6.b">
+<tool id="fuma" name="FuMa" version="2.7.1.a">
 	<description>FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).</description>
 	
 	<requirements>
-		<requirement type="package" version="2.6.6">fuma</requirement>
+		<requirement type="package" version="2.7.1">fuma</requirement>
 	</requirements>
 	
 	<version_command>fuma --version</version_command><!-- -V also works, but is not GNU standard -->
@@ -36,8 +36,19 @@
 		    $samples_str
 		  -l
 		    $links_str
+		#if $output_format == "list_boolean"
+		  -f list
+		#else
 		  -f $output_format
-		  -o $fuma_overview
+		#end if
+		  -o $fuma_overview ; 
+		
+		
+		
+		#if $output_format == "list_boolean"
+			fuma-list-to-boolean-list -o tmp.txt $fuma_overview &amp;&amp;
+			mv tmp.txt $fuma_overview
+		#end if
 	</command>
 	
 	<inputs>
@@ -46,21 +57,22 @@
 			<param name="format" type="select" label="Format of dataset">
 				<option value="chimerascan">ChimeraScan</option>
 				<option value="defuse">DeFuse</option>
-				<option value="completegenomics">Complete Genomics</option>
-				<option value="tophatfusionpostpotentialfusion">Tophat Fusion Post (potential fusion file)</option>
-				<option value="tophatfusionpostresult">Tophat Fusion Post (result file)</option>
-				<option value="tophatfusionpre">Tophat Fusion Pre (final list file)</option>
-				<option value="fusioncatcherfinal">FusionCatcher (final-list file)</option>
+				<option value="complete-genomics">Complete Genomics</option>
+				<option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>
 				<option value="fusionmap">FusionMap</option>
-				<option value="rnastarchimeric">STAR (chimeric file)</option>
-				<option value="oncofuse">Oncofuse</option>
-				<option value="trinitygmap">GMAP (As step after Trinity)</option>
+				<option value="trinity-gmap">GMAP (As step after Trinity)</option>
+				<option value="oncofuse">OncoFuse</option>
+				<option value="rna-star_chimeric">STAR (chimeric file)</option>
+				<option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>
+				<option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>
+				<option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>
 			</param>
 			<param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene annotations! Gene annotations should only be different if different reference genome builds were used." />
 		</repeat>
 		
 		<param name="output_format" type="select" label="Output format">
-			<option value="list" selected="true">List</option>
+			<option value="list_boolean" selected="true">List (Boolean)</option>
+			<option value="list">List</option>
 			<option value="summary">Count summary</option>
 		</param>
 	</inputs>
@@ -98,6 +110,59 @@
 		</test>
 	</tests>
 	
-	<help>
+	<help>============
+Introduction
+============
+
+FuMa (Fusion Matcher) matches predicted fusion events (both genomic and transcriptomic) according to chromosomal location or assocatiated gene annotation(s) where the latter should be genome build inspecific.
+
+Because RNA-Sequencing deals with samples that may have undergrond splicing, reads may split up because of biological processes. If a fusion event takes place, the same thing may happen. Therefore we hypothesize that using spanning read distances may be unreliable, because there are known introns of > 100kb. Therefore, FuMa translates the breakpoint to gene names, and only overlaps breakpoints with the same genename(s).
+
+=====
+Usage
+=====
+
+After you have uploaded the results of your Fusion Gene detection experiment, and selected the format to be *tabular*, you can start the FuMa wrapper. For each dataset you simply have to add another repeat. Then you have to select a corresponding format:
+
+*******
+Formats
+*******
+
++-------------------+-----------------------+-------------------------------------+
+|Tools              | File                  | Format string                       |
++===================+=======================+=====================================+
+|ChimeraScan        | chimeras.bedpe        | chimerascan                         |
++-------------------+-----------------------+-------------------------------------+
+|Complete Genomics  | highConfidenceJu*.tsv | complete-genomics                   |
++-------------------+-----------------------+-------------------------------------+
+|Complete Genomics  | allJunctionsBeta*.tsv | complete-genomics                   |
++-------------------+-----------------------+-------------------------------------+
+|DeFuse             | results.txt           | defuse                              |
++-------------------+-----------------------+-------------------------------------+
+|DeFuse             | results.classify.txt  | defuse                              |
++-------------------+-----------------------+-------------------------------------+
+|DeFuse             | results.filtered.txt  | defuse                              |
++-------------------+-----------------------+-------------------------------------+
+|Fusion Catcher     | final-list_cand*.txt  | fusion-catcher_final                |
++-------------------+-----------------------+-------------------------------------+
+|FusionMap          |                       | fusionmap                           |
++-------------------+-----------------------+-------------------------------------+
+|Trinity + GMAP     |                       | trinity-gmap                        |
++-------------------+-----------------------+-------------------------------------+
+|OncoFuse           |                       | oncofuse                            |
++-------------------+-----------------------+-------------------------------------+
+|RNA STAR           | Chimeric.out.junction | rna-star_chimeric                   |
++-------------------+-----------------------+-------------------------------------+
+|TopHat Fusion pre  | fusions.out           | tophat-fusion_pre                   |
++-------------------+-----------------------+-------------------------------------+
+|TopHat Fusion post | potential_fusion.txt  | tophat-fusion_post_potential_fusion |
++-------------------+-----------------------+-------------------------------------+
+|TopHat Fusion post | result.txt            | tophat-fusion_post_result           |
++-------------------+-----------------------+-------------------------------------+
+
+To annotate genes upon the breakpoints you must provide a BED file that contains gene annotations for the user genome build. Make sure **your BED file contains one gene per line**. You should use BED files that contain one exon per line only if you want restrict your analysis to fusion genes detected within exons.
+
+UCSC genome browser provides a very simple way of obtaining BED files with one gene per line by selecting their *RefSeq Genes*-track and *knownGene*-table and putting the export format to BED. Galaxy should have a built-in UCSC table browser.
+
 	</help>
 </tool>
diff -r 76293f7745ff -r f06461883f7b tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 29 05:28:17 2015 -0400
+++ b/tool_dependencies.xml	Thu Apr 02 08:06:04 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-	<package name="fuma" version="2.6.6">
+	<package name="fuma" version="2.7.1">
 		<install version="1.0">
 			<actions>
 				<action type="make_directory">$INSTALL_DIR/lib/python</action>
@@ -9,7 +9,7 @@
 				<action type="shell_command">
 					git clone https://github.com/yhoogstrate/fuma.git fuma &amp;&amp;
 					cd fuma &amp;&amp;
-					git reset --hard 433d68af9a1b113bd0ae09c2b80279c589ac2d5a &amp;&amp;
+					git reset --hard 3d9a0532209d4ad10283cac324788b4fecfd2675 &amp;&amp;
 					
 					export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
 					python setup.py build &amp;&amp;