changeset 0:267d0c2ebe56 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fuma.xml	Sat Mar 21 02:59:14 2015 -0400
@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="fuma" name="FuMa" version="2.6.3.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="2.6.3">fuma</requirement>
+	</requirements>
+	
+	<version_command>fuma --version</version_command><!-- -V also works, but is not GNU standard -->
+	
+	<command>
+		#import pipes
+		
+		#set $gene_annotations = []
+		#set $samples = []
+		#set $links = []
+		
+		#for $i, $d in enumerate( $datasets )
+			
+			#set $sample_name = pipes.quote(str($d['sample'].name))
+			
+			#set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d['gene_annotation'].file_name) ]
+			
+			#set $samples = $samples + [ $sample_name + ":" + str($d['format']) + ":" + str($d['sample'].file_name) ]
+			#set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]
+		#end for
+		
+		#set $gene_annotations_str = " ".join(gene_annotations)
+		#set $samples_str = " ".join(samples)
+		#set $links_str = " ".join(links)
+		
+		fuma 
+		  -a
+		    $gene_annotations_str
+		  -s
+		    $samples_str
+		  -l
+		    $links_str
+		  -f 'list'
+		  -o $fuma_overview
+	</command>
+	
+	<inputs>
+		<repeat name="datasets" title="FusionGene Datasets" min="2">
+			<param name="sample" type="data" format="txt, tabular" label="Dataset ()" />
+			<param name="format" type="select" label="Format of dataset">
+				<option value="chimerascan">ChimeraScan</option>
+				<option value="defuse">DeFuse</option>
+				<option value="completegenomics">Complete Genomics</option>
+				<option value="tophatfusionpostpotentialfusion">Tophat Fusion Post (potential fusion file)</option>
+				<option value="tophatfusionpostresult">Tophat Fusion Post (result file)</option>
+				<option value="tophatfusionpre">Tophat Fusion Pre (final list file)</option>
+				<option value="fusioncatcherfinal">FusionCatcher (final-list file)</option>
+				<option value="fusionmap">FusionMap</option>
+				<option value="rnastarchimeric">STAR (chimeric file)</option>
+				<option value="oncofuse">Oncofuse</option>
+				<option value="trinitygmap">GMAP (As step after Trinity)</option>
+			</param>
+			<param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene names if different gene names are being used." />
+		</repeat>
+	</inputs>
+	
+	<outputs>
+		<data format="tabular" name="fuma_overview" label="${tool.name} on ${', '.join([ str(d['sample'].hid)+': '+d['sample'].name for d in $datasets ])}" />
+	</outputs>
+	
+	<help>
+	</help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Mar 21 02:59:14 2015 -0400
@@ -0,0 +1,29 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="fuma" version="2.6.3">
+		<install version="1.0">
+			<actions>
+				<action type="make_directory">$INSTALL_DIR/lib/python</action>
+				<action type="make_directory">$INSTALL_DIR/lib64/python</action>
+				
+				<action type="shell_command">
+					git clone https://github.com/yhoogstrate/fuma.git fuma &amp;&amp;
+					cd fuma &amp;&amp;
+					git reset --hard 7d22741f37549eb65b85136316ca0dd2cda529ec &amp;&amp;
+					
+					export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp;
+					python setup.py build &amp;&amp;
+					python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
+				</action>
+				
+				<action type="set_environment">
+					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+		<readme>
+			Downloads and installs Fuma; requires python pip and get to be installed.
+		</readme>
+	</package>
+</tool_dependency>