--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iReport.sh	Tue Jul 01 11:42:23 2014 -0400
@@ -0,0 +1,82 @@
+#!/bin/bash
+repositorypath="/mnt/galaxyTools/shed_tools/toolshed.nbic.nl/repos/saskia-hiltemann/ireport/71dc132e9bb2/ireport"  # TODO: dependency
+source "${repositorypath}/createHTML.sh"
+
+echo "allparams: $@"
+function usage() { echo "Oops!"; }
+
+
+# set some defaults
+
+
+set -- `getopt -n$0 -u -a --longoptions="ifusepath: galaxypath: tab: item: htmlout: label: toolpath: minwidth: coverimage:" "h:" "$@"` || usage
+[ $# -eq 0 ] && usage
+
+while [ $# -gt 0 ]
+do
+    case "$1" in
+       	--toolpath)      		repositorypath=$2;shift;;  
+		--galaxypath)			galaxypath=$2;shift;; 
+		--minwidth)				minwidth=$2;shift;; 
+		--tab)					tabs+=",$2";shift;;
+		--item)					items+=",$2";shift;;
+		--htmlout)				htmlout=$2;shift;;
+		--label)				title="$@";shift;;
+		--coverimage)			coverimage=$2;shift;;
+        -h)        	shift;;
+		--)        	shift;break;;
+        -*)        	usage;;
+        *)         	break;;
+    esac
+    shift
+done
+
+
+mkdir $galaxypath
+
+tabs=${tabs//,/ }; tabs=${tabs/ /}
+items=${items//,/ }; items=${items/ /}
+title=${title//--/}
+title=${title//label/}
+echo -e "\n"
+echo -e "title:      $title"
+echo -e "tabs:       $tabs"
+echo -e "items:      $items"
+echo -e "htmlout:    $htmlout"
+echo -e "coverimage: $coverimage"
+echo -e "\n"
+
+for i in $tabs
+do 
+	echo "tabname: $i" 
+done
+
+coverimage=${coverimage:1}
+echo -e "coverimage2: $coverimage"
+
+#if no coverimage provided, use default EMC logo
+if [[ -z $coverimage ]] 
+then
+	cp $repositorypath/intro.jpg ${galaxypath}/intro.jpg
+	coverimage="intro.jpg"
+fi
+echo -e "coverimage3: $coverimage"
+
+## Copy supporting files to output directory
+cp ${repositorypath}/jquery.dataTables.css ${galaxypath}/jquery.dataTables.css
+cp ${repositorypath}/jquery.dataTables.js ${galaxypath}/jquery.dataTables.js
+cp -R ${repositorypath}/iframe-resizer/ ${galaxypath}/iframe-resizer/
+cp -R ${repositorypath}/DataTables-1.9.4/ ${galaxypath}/DataTables-1.9.4/
+cp ${repositorypath}/jquery.zoom.js ${galaxypath}/jquery.zoom.js
+
+
+echo "done copying resource files"
+ls ${galaxypath}
+
+
+## Create cover HTML page
+makeIntroPage "$title" $coverimage "report.html" $htmlout
+
+## Create Report page with tabs
+createMainPage ${galaxypath}/report.html "$tabs" "$items" $minwidth
+