--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igvscreenshot.xml	Tue Jul 28 11:16:53 2015 -0400
@@ -0,0 +1,84 @@
+<tool id="igvscreenshot" name="Take an IGV screenshot" version="1.2">
+
+	<description>specifying tracks and a genomic location</description> 
+
+        <requirements>		
+		<requirement type="package" version="2.3.57">igv</requirement>
+	</requirements>
+        
+	
+	<command interpreter="bash">
+		igvscreenshot.sh 
+                    --build $reference
+                    #for $i, $t in enumerate( $tracks )
+                        --track ${t.inputfile}
+                        --ftype ${t.inputfile.extension}
+                        --view ${t.view}
+                        --viewaspairs ${t.viewaspairs}
+                        #if not $t.trackname  <!-- validator for empty field does not seem to work within a repeat, so this is the workaround  -->
+                            #set $tracklabel = "noname"
+                        #else
+                            #set $tracklabel = $t.trackname
+                        #end if
+                        --label $tracklabel
+                        #if $t.inputfile.extension == "bam"
+                            --index $t.inputfile.metadata.bam_index
+                        #else
+                            --index "none"
+                        #end if
+                    #end for
+                    --region "$region"       
+	</command>
+
+
+	<inputs>
+	<!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions -->
+                
+                <param name="reference" type="select" label="Select Build">
+                    <option value="hg18"> hg18 </option>
+                    <option value="hg19"> hg19 </option>
+		</param>
+                
+		<!-- file from history -->
+                <repeat name="tracks" title="Track" min="1">
+                    <param name="inputfile" type="data" format="bam,vcf,bed,gtf,gff" label="Select input file" help="choose input file from history"/>
+                    <param name="trackname" type="text" size="100" value="track label" label="Track Label" >
+                        <sanitizer>
+				<valid initial="default"> 
+					<add preset="string.printable"/> 
+					<remove value=" "/>
+				</valid> 
+				<mapping initial="none"> 
+					<add source=" " target="_"/>
+				</mapping> 
+			</sanitizer>                        
+                    </param>
+                    <param name="view" type="select" label="View settings of track" >
+                           <option value="collapse"  > collapsed </option>
+                           <option value="expand"  > expanded </option>
+                           <option value="squish"  > squished </option>
+                    </param>                    
+                    <param name="viewaspairs" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="view as pairs?" help="optional setting for paired-end data"/>
+				
+                </repeat>
+                <!-- text field parameter -->
+		<param name="region" type="text" size="100" value="chr:start-end" label="Enter region to visualise in IGV, format chr:start-end" help="to show multiple regions in a single image, use comma-separated list of regions, e.g. chr1:0-100,chr2:100-200"/>
+    
+                </inputs>
+
+	
+	<outputs>
+		<data format="png" name="outputfile" from_work_dir="screenshot.png" label="IGV screenshot of region ${region} on ${on_string}"/>
+	</outputs>
+
+	<help>
+This tool will create an IGV screenshot of the desired location(s) with the desired tracks.
+        
+Tracks may be bam, vcf, bed, gff or gtf format.
+
+Multiple regions may be specified (comma-separated)
+
+
+        
+        </help>
+</tool>
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