# HG changeset patch
# User ngsplot
# Date 1426707834 14400
# Node ID b2d5006b82b8ca3b6229cb0afd745a91a47295be
# Parent  795270a5555cfbee2fbb8ddd66b3db0c0fe5e9ae
Uploaded

diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed/ngsplot_intro/intro.xml
--- a/ngsplot_galaxytoolshed/ngsplot_intro/intro.xml	Wed Mar 18 15:06:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<tool id="ngs.plot_intro" name="Introduction">
-<command interpreter="perl">
-
-</command>
-
-#if $numsamples.numsamples2 == "1":
-   runNGSplot.pl 
-   $genome_name 
-
-#else if $numsamples.numsamples2 == "5":
-   runNGSplot.pl 
-   $genome_name 
-
-#end if:
-
-<!--
-<inputs>
-   <param  type="text" value="mm9" name="genome_name" label="Intro Text here..." help="" >
-   </param>
-</inputs>
--->
-
-<help>
-
-**WELCOME TO NGS.PLOT ON GALAXY**
-
------
-
-**HOW TO USE**
-
-To use ngs.plot here on this GUI-based galaxy implementation, first upload your alignment BAM file(s) using the *Get Data* -> **Upload File** tool on top of the left panel of this page. The names of your uploaded file(s) will then be displayed on the right panel. Next, select the *NGS.PLOT V2.47.1* -> **ngs.plot** tool on the left panel and all other input information required from you will be displayed as a form on the main central panel. Complete the form then click the *Execute* button to launch the program. Three output files (a profile chart, a heatmap, and a zipped data file) will be generated and displayed on the right panel, which you can click on to view. To further replot the figures into a format that you desire, use the *NGS.PLOT V2.47.1* -> **replot** tool with it's input file being the zip file previously generated by 'ngs.plot'.
-
-For a more detailed explanation of how to run ngs.plot on Galaxy, please see the tutorial at https://code.google.com/p/ngsplot/wiki/webngsplot. 
-
------
-
-**INTRODUCTION**
-
-ngs.plot is a program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
-
-DNA sequencing is at the core of genomics. The NGS technology has been tremendously improved in the past few years. It can now determine more than a billion DNA sequences within a week, generating terabytes of data. Applications include but are not limited to: 1. ChIP-seq which profiles genome-wide protein-DNA interactions; 2. RNA-seq which measures the gene expression levels. It is very helpful to look at the enrichment of those sequences at various functional regions. Although a genome browser (such as the UCSC genome browser) allows a researcher to visualize these data, it limits the view to a slice of the genome. While the genome is like a huge collection of functional elements that can be classified into different categories. Each category of elements may perform distinct functions and they might further contain modules.
-
-The signature advantage of ngs.plot is that it collects a large database of functional elements for many genomes. A user can ask for a functionally important region to be displayed in one command. It handles large sequencing data efficiently and has only modest memory requirement. For example, ngs.plot was used to draw a plot for all the genes on the mouse genome from 71GB of ChIP-seq data in 25 min, with a memory footprint of 2.7GB using 4 x 2.4GHz CPU cores. ngs.plot is also easy to use. A user only needs to create a very small text file called configuration, telling the program which samples to look at and how they should be combined with different regions, and then run the program with one command. This Galaxy web-based version of ngs.plot is also available for users not familiar with command-line programs. For additional program details, please refer to our project homepage at https://code.google.com/p/ngsplot or to the publication cited below. 
-
------
-
-**COMMERCIAL USE**
-
-ngs.plot is free for use by academic users. If you want to use it in commercial settings, please contact Lisa Placanica at: lisa.placanica@mssm.edu
-
-**HOW TO CITE**
-
-Shen, L.*, Shao, N., Liu, X. and Nestler, E. (2014) ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases, BMC Genomics, 15, 284.
-
-**CONTACT**
-
-ngs.plot is developed by Drs. Li Shen, Ningyi Shao and Xiaochuan Liu at the Icahn School of Medicine at Mount Sinai. If you have technical questions about ngs.plot, please use the discussion forum. For collaborations or any other matters, use: li.shen AT mssm.edu.
-
-</help>
-<outputs>
-<!--
-   <data format="pdf" name="out_avg_png" />
-   <data format="pdf" name="out_hm_png" />
-   <data format="zip" name="out_zip"/>
--->
-</outputs>
-</tool>
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed/ngsplot_main/ngsplot.xml
--- a/ngsplot_galaxytoolshed/ngsplot_main/ngsplot.xml	Wed Mar 18 15:06:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3174 +0,0 @@
-<tool id="ngs.plot" name="ngs.plot">
-<command interpreter="perl">
-#if $numsamples.numsamples2 == "1":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "2":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "3":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "4":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-   
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "5":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-
-   $numsamples.usepair.bamfile5
-   $numsamples.usepair.reffile5
-   $numsamples.usepair.genelist5.usegenelist5
-   $numsamples.usepair.genelist5.genelist5
-   $numsamples.usepair.title5
-   $numsamples.usepair.fraglen5
-   $numsamples.usepair.linecol5
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "6":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-
-   $numsamples.usepair.bamfile5
-   $numsamples.usepair.reffile5
-   $numsamples.usepair.genelist5.usegenelist5
-   $numsamples.usepair.genelist5.genelist5
-   $numsamples.usepair.title5
-   $numsamples.usepair.fraglen5
-   $numsamples.usepair.linecol5
-
-   $numsamples.usepair.bamfile6
-   $numsamples.usepair.reffile6
-   $numsamples.usepair.genelist6.usegenelist6
-   $numsamples.usepair.genelist6.genelist6
-   $numsamples.usepair.title6
-   $numsamples.usepair.fraglen6
-   $numsamples.usepair.linecol6
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "7":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-
-   $numsamples.usepair.bamfile5
-   $numsamples.usepair.reffile5
-   $numsamples.usepair.genelist5.usegenelist5
-   $numsamples.usepair.genelist5.genelist5
-   $numsamples.usepair.title5
-   $numsamples.usepair.fraglen5
-   $numsamples.usepair.linecol5
-
-   $numsamples.usepair.bamfile6
-   $numsamples.usepair.reffile6
-   $numsamples.usepair.genelist6.usegenelist6
-   $numsamples.usepair.genelist6.genelist6
-   $numsamples.usepair.title6
-   $numsamples.usepair.fraglen6
-   $numsamples.usepair.linecol6
-
-   $numsamples.usepair.bamfile7
-   $numsamples.usepair.reffile7
-   $numsamples.usepair.genelist7.usegenelist7
-   $numsamples.usepair.genelist7.genelist7
-   $numsamples.usepair.title7
-   $numsamples.usepair.fraglen7
-   $numsamples.usepair.linecol7
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "8":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-
-   $numsamples.usepair.bamfile5
-   $numsamples.usepair.reffile5
-   $numsamples.usepair.genelist5.usegenelist5
-   $numsamples.usepair.genelist5.genelist5
-   $numsamples.usepair.title5
-   $numsamples.usepair.fraglen5
-   $numsamples.usepair.linecol5
-
-   $numsamples.usepair.bamfile6
-   $numsamples.usepair.reffile6
-   $numsamples.usepair.genelist6.usegenelist6
-   $numsamples.usepair.genelist6.genelist6
-   $numsamples.usepair.title6
-   $numsamples.usepair.fraglen6
-   $numsamples.usepair.linecol6
-
-   $numsamples.usepair.bamfile7
-   $numsamples.usepair.reffile7
-   $numsamples.usepair.genelist7.usegenelist7
-   $numsamples.usepair.genelist7.genelist7
-   $numsamples.usepair.title7
-   $numsamples.usepair.fraglen7
-   $numsamples.usepair.linecol7
-
-   $numsamples.usepair.bamfile8
-   $numsamples.usepair.reffile8
-   $numsamples.usepair.genelist8.usegenelist8
-   $numsamples.usepair.genelist8.genelist8
-   $numsamples.usepair.title8
-   $numsamples.usepair.fraglen8
-   $numsamples.usepair.linecol8
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "9":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-
-   $numsamples.usepair.bamfile5
-   $numsamples.usepair.reffile5
-   $numsamples.usepair.genelist5.usegenelist5
-   $numsamples.usepair.genelist5.genelist5
-   $numsamples.usepair.title5
-   $numsamples.usepair.fraglen5
-   $numsamples.usepair.linecol5
-
-   $numsamples.usepair.bamfile6
-   $numsamples.usepair.reffile6
-   $numsamples.usepair.genelist6.usegenelist6
-   $numsamples.usepair.genelist6.genelist6
-   $numsamples.usepair.title6
-   $numsamples.usepair.fraglen6
-   $numsamples.usepair.linecol6
-
-   $numsamples.usepair.bamfile7
-   $numsamples.usepair.reffile7
-   $numsamples.usepair.genelist7.usegenelist7
-   $numsamples.usepair.genelist7.genelist7
-   $numsamples.usepair.title7
-   $numsamples.usepair.fraglen7
-   $numsamples.usepair.linecol7
-
-   $numsamples.usepair.bamfile8
-   $numsamples.usepair.reffile8
-   $numsamples.usepair.genelist8.usegenelist8
-   $numsamples.usepair.genelist8.genelist8
-   $numsamples.usepair.title8
-   $numsamples.usepair.fraglen8
-   $numsamples.usepair.linecol8
-
-   $numsamples.usepair.bamfile9
-   $numsamples.usepair.reffile9
-   $numsamples.usepair.genelist9.usegenelist9
-   $numsamples.usepair.genelist9.genelist9
-   $numsamples.usepair.title9
-   $numsamples.usepair.fraglen9
-   $numsamples.usepair.linecol9
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#else if $numsamples.numsamples2 == "10":
-   runNGSplot.pl 
-   $genome_name 
-   $genomic_region_source_type.genomic_region 
-   $genomic_region_source_type.further_information 
-   $genomic_region_source_type.interval_size 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
-   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
-   $numsamples.numsamples2
-   $numsamples.usepair.usepair1
-
-   $numsamples.usepair.bamfile1
-   $numsamples.usepair.reffile1
-   $numsamples.usepair.genelist1.usegenelist1
-   $numsamples.usepair.genelist1.genelist1
-   $numsamples.usepair.title1
-   $numsamples.usepair.fraglen1
-   $numsamples.usepair.linecol1
-
-   $numsamples.usepair.bamfile2
-   $numsamples.usepair.reffile2
-   $numsamples.usepair.genelist2.usegenelist2
-   $numsamples.usepair.genelist2.genelist2
-   $numsamples.usepair.title2
-   $numsamples.usepair.fraglen2
-   $numsamples.usepair.linecol2
-
-   $numsamples.usepair.bamfile3
-   $numsamples.usepair.reffile3
-   $numsamples.usepair.genelist3.usegenelist3
-   $numsamples.usepair.genelist3.genelist3
-   $numsamples.usepair.title3
-   $numsamples.usepair.fraglen3
-   $numsamples.usepair.linecol3
-
-   $numsamples.usepair.bamfile4
-   $numsamples.usepair.reffile4
-   $numsamples.usepair.genelist4.usegenelist4
-   $numsamples.usepair.genelist4.genelist4
-   $numsamples.usepair.title4
-   $numsamples.usepair.fraglen4
-   $numsamples.usepair.linecol4
-
-   $numsamples.usepair.bamfile5
-   $numsamples.usepair.reffile5
-   $numsamples.usepair.genelist5.usegenelist5
-   $numsamples.usepair.genelist5.genelist5
-   $numsamples.usepair.title5
-   $numsamples.usepair.fraglen5
-   $numsamples.usepair.linecol5
-
-   $numsamples.usepair.bamfile6
-   $numsamples.usepair.reffile6
-   $numsamples.usepair.genelist6.usegenelist6
-   $numsamples.usepair.genelist6.genelist6
-   $numsamples.usepair.title6
-   $numsamples.usepair.fraglen6
-   $numsamples.usepair.linecol6
-
-   $numsamples.usepair.bamfile7
-   $numsamples.usepair.reffile7
-   $numsamples.usepair.genelist7.usegenelist7
-   $numsamples.usepair.genelist7.genelist7
-   $numsamples.usepair.title7
-   $numsamples.usepair.fraglen7
-   $numsamples.usepair.linecol7
-
-   $numsamples.usepair.bamfile8
-   $numsamples.usepair.reffile8
-   $numsamples.usepair.genelist8.usegenelist8
-   $numsamples.usepair.genelist8.genelist8
-   $numsamples.usepair.title8
-   $numsamples.usepair.fraglen8
-   $numsamples.usepair.linecol8
-
-   $numsamples.usepair.bamfile9
-   $numsamples.usepair.reffile9
-   $numsamples.usepair.genelist9.usegenelist9
-   $numsamples.usepair.genelist9.genelist9
-   $numsamples.usepair.title9
-   $numsamples.usepair.fraglen9
-   $numsamples.usepair.linecol9
-
-   $numsamples.usepair.bamfile10
-   $numsamples.usepair.reffile10
-   $numsamples.usepair.genelist10.usegenelist10
-   $numsamples.usepair.genelist10.genelist10
-   $numsamples.usepair.title10
-   $numsamples.usepair.fraglen10
-   $numsamples.usepair.linecol10
-
-   $gene_database
-   $randomly_sample
-   $GO.gene_order
-   $GO.KNC
-   $GO.MIT
-   $GO.NRS
-   $chunk_size
-   $quality_requirement
-   $standard_error
-   $radius_size
-   $flooding_fraction
-   $smooth_method
-   $shaded_area
-   $out_zip  $out_avg_png  $out_hm_png
-
-#end if:
-
-</command>
-
-<!-->
-<-->
-
-<inputs>
-   <param  type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" >
-   </param>
-   <conditional name="genomic_region_source_type">
-      <param type="select" name="genomic_region" label="Genomic region" help="">
-         <option value="tss">TSS</option>
-         <option value="tes">TES</option>
-         <option value="genebody">Genebody</option>
-         <option value="exon">Exon</option>
-         <option value="cgi">CGI</option>
-         <option value="bed">Customized bed file</option>
-      </param>
-
-      <when value="tss"> 
-         <param type="select" name="further_information"  label="Further information: Not required for TSS">
-            <option value="na">Not Required</option>
-         </param>
-         <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
-            <option value="na">Not Required</option>
-         </param>
-         <conditional name="flanking_region_option_source_type">
-            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
-               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
-               <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
-            </param>
-            <when value="flanking_region_size">
-               <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
-            </when>
-            <!--when value="flanking_floating_size">
-               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
-            </when-->
-         </conditional>
-      </when> 
-      <when value="tes"> 
-         <param type="select" name="further_information"  label="Further information: Not required for TES">
-            <option value="na">Not Required</option>
-         </param>
-         <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
-            <option value="na">Not Required</option>
-         </param>
-         <conditional name="flanking_region_option_source_type">
-            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
-               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
-               <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
-            </param>
-            <when value="flanking_region_size">
-               <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
-            </when>
-            <!--when value="flanking_floating_size">
-               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
-            </when-->
-         </conditional>
-      </when> 
-      <when value="genebody"> 
-         <param type="select" name="further_information"  label="You selected Genebody, further information can be provided for specific regions to plot">
-            <option value="chipseq">ChIP-seq</option>
-            <option value="rnaseq">RNA-seq</option>
-         </param>
-         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
-            <option value="automatic">Default</option>
-            <option value="0">Small</option>
-            <option value="1">Large</option>
-         </param>
-         <conditional name="flanking_region_option_source_type">
-            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
-               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
-               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
-            </param>
-            <when value="flanking_region_size">
-               <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
-            </when>
-            <when value="flanking_floating_size">
-               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
-            </when>
-         </conditional>            
-      </when>
-      <when value="exon"> 
-         <param type="select" name="further_information"  label="You selected Exon, further information can be provided for specific regions to plot">
-            <option value="canonical">Canonical</option>
-            <option value="variant">Variant</option>
-            <option value="promoter">Promoter</option>
-            <option value="polyA">polyA</option>
-            <option value="altAcceptor">altAcceptor</option>
-            <option value="altDonor">altDonor</option>
-            <option value="altBoth">altBoth</option>
-         </param>
-         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
-            <option value="automatic">Default</option>
-            <option value="0">Small</option>
-            <option value="1">Large</option>
-         </param>
-         <conditional name="flanking_region_option_source_type">
-            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
-               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
-               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
-            </param>
-            <when value="flanking_region_size">
-               <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
-            </when>
-            <when value="flanking_floating_size">
-               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
-            </when>
-         </conditional>
-      </when>
-      <when value="cgi"> 
-         <param type="select" name="further_information"  label="You select CGI, further information can be provided for specific regions to plot">
-            <option value="ProximalPromoter">ProximalPromoter</option>
-            <option value="Genebody">GeneBody</option>
-            <option value="Genedesert">GeneDesert</option>
-            <option value="OtherIntergenic">OtherIntergenic</option>
-            <option value="Pericentromere">Pericentromere</option>
-            <option value="Subtelomere">Subtelomere</option>
-            <option value="Promoter1k">Promoter1k</option>
-            <option value="Promoter3k">Promoter3k</option>
-         </param>
-         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
-            <option value="automatic">Default</option>
-            <option value="0">Small</option>
-            <option value="1">Large</option>
-         </param>
-         <conditional name="flanking_region_option_source_type">
-            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
-               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
-               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
-            </param>
-            <when value="flanking_region_size">
-               <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
-            </when>
-            <when value="flanking_floating_size">
-               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
-            </when>
-         </conditional>
-      </when> 
-      <when value="bed"> 
-         <param type="select" name="further_information"  label="Further information: Not required for bed input">
-            <option value="na">Not Required</option>
-         </param>
-         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
-            <option value="automatic">Default</option>
-            <option value="0">Small</option>
-            <option value="1">Large</option>
-         </param>
-         <conditional name="flanking_region_option_source_type">
-            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
-               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
-               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
-            </param>
-            <when value="flanking_region_size">
-               <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
-            </when>
-            <when value="flanking_floating_size">
-               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
-            </when>
-         </conditional>
-      </when> 
-   </conditional>
-
-
-   <conditional name="numsamples">
-      <param type="select" name="numsamples2" label="Number of samples to plot">
-         <option value="1">1</option>
-         <option value="2">2</option>
-         <option value="3">3</option>
-         <option value="4">4</option>
-         <option value="5">5</option>
-         <option value="6">6</option>
-         <option value="7">7</option>
-         <option value="8">8</option>
-         <option value="9">9</option>
-         <option value="10">10</option>
-      </param>
-
-      <when value="1">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 1 sample, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 1 sample, no refpairs, entry 1-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 1 sample, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 1 sample, yes refpairs, entry 1-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="2">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 2 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 2 samples, no refpairs, entry 1-->
-               <!-- START: 2 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 2 samples, no refpairs, entry 2-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 2 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 2 samples, yes refpairs, entry 1-->
-               <!-- START: 2 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 2 samples, yes refpairs, entry 2-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="3">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 3 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 3 samples, no refpairs, entry 1-->
-               <!-- START: 3 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 3 samples, no refpairs, entry 2-->
-               <!-- START: 3 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 3 samples, no refpairs, entry 3-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 3 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 3 samples, yes refpairs, entry 1-->
-               <!-- START: 3 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 3 samples, yes refpairs, entry 2-->
-               <!-- START: 3 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 3 samples, yes refpairs, entry 2-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="4">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 4 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 4 samples, no refpairs, entry 1-->
-               <!-- START: 4 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 4 samples, no refpairs, entry 2-->
-               <!-- START: 4 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 4 samples, no refpairs, entry 3-->
-               <!-- START: 4 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 4 samples, no refpairs, entry 4-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 4 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 4 samples, yes refpairs, entry 1-->
-               <!-- START: 4 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 4 samples, yes refpairs, entry 2-->
-               <!-- START: 4 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 4 samples, yes refpairs, entry 3-->
-               <!-- START: 4 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 4 samples, yes refpairs, entry 4-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="5">           
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 5 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 5 samples, no refpairs, entry 1-->
-               <!-- START: 5 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 5 samples, no refpairs, entry 2-->
-               <!-- START: 5 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 5 samples, no refpairs, entry 3-->
-               <!-- START: 5 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 5 samples, no refpairs, entry 4-->
-               <!-- START: 5 samples, no refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="hidden"  name="reffile5" value="na"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 5 samples, no refpairs, entry 5-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 5 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 5 samples, yes refpairs, entry 1-->
-               <!-- START: 5 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 5 samples, yes refpairs, entry 2-->
-               <!-- START: 5 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 5 samples, yes refpairs, entry 3-->
-               <!-- START: 5 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 5 samples, yes refpairs, entry 4-->
-               <!-- START: 5 samples, yes refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 5 samples, yes refpairs, entry 5-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="6">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?"  help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 6 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 6 samples, no refpairs, entry 1-->
-               <!-- START: 6 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 6 samples, no refpairs, entry 2-->
-               <!-- START: 6 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 6 samples, no refpairs, entry 3-->
-               <!-- START: 6 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 6 samples, no refpairs, entry 4-->
-               <!-- START: 6 samples, no refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="hidden"  name="reffile5" value="na"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 6 samples, no refpairs, entry 5-->
-               <!-- START: 6 samples, no refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="hidden"  name="reffile6" value="na"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 6 samples, no refpairs, entry 6-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 6 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 6 samples, yes refpairs, entry 1-->
-               <!-- START: 6 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 6 samples, yes refpairs, entry 2-->
-               <!-- START: 6 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 6 samples, yes refpairs, entry 3-->
-               <!-- START: 6 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 6 samples, yes refpairs, entry 4-->
-               <!-- START: 6 samples, yes refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 6 samples, yes refpairs, entry 5-->
-               <!-- START: 6 samples, yes refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 6 samples, yes refpairs, entry 6-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="7">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 7 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 1-->
-               <!-- START: 7 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 2-->
-               <!-- START: 7 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 3-->
-               <!-- START: 7 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 4-->
-               <!-- START: 7 samples, no refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="hidden"  name="reffile5" value="na"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 5-->
-               <!-- START: 7 samples, no refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="hidden"  name="reffile6" value="na"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 6-->
-               <!-- START: 7 samples, no refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="hidden"  name="reffile7" value="na"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 7 samples, no refpairs, entry 7-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 7 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 1-->
-               <!-- START: 7 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 2-->
-               <!-- START: 7 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 3-->
-               <!-- START: 7 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 4-->
-               <!-- START: 7 samples, yes refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 5-->
-               <!-- START: 7 samples, yes refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 6-->
-               <!-- START: 7 samples, yes refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 7 samples, yes refpairs, entry 7-->
-            </when> 
-         </conditional>
-     </when>                     
-      <when value="8">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 8 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 1-->
-               <!-- START: 8 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 2-->
-               <!-- START: 8 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 3-->
-               <!-- START: 8 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 4-->
-               <!-- START: 8 samples, no refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="hidden"  name="reffile5" value="na"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 5-->
-               <!-- START: 8 samples, no refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="hidden"  name="reffile6" value="na"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 6-->
-               <!-- START: 8 samples, no refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="hidden"  name="reffile7" value="na"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 7-->
-               <!-- START: 8 samples, no refpairs, entry 8-->
-               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
-               <param  type="hidden"  name="reffile8" value="na"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist8"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
-               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
-               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
-               <!-- END: 8 samples, no refpairs, entry 8-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 8 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 1-->
-               <!-- START: 8 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 2-->
-               <!-- START: 8 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 3-->
-               <!-- START: 8 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 4-->
-               <!-- START: 8 samples, yes refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 5-->
-               <!-- START: 8 samples, yes refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 6-->
-               <!-- START: 8 samples, yes refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 7-->
-               <!-- START: 8 samples, yes refpairs, entry 8-->
-               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
-               <param  type="data"  name="reffile8" label="Sample 8: Reference BAM file"/>  
-               <conditional name="genelist8">
-                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist8"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
-               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
-               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
-               <!-- END: 8 samples, yes refpairs, entry 8-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="9">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 9 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 1-->
-               <!-- START: 9 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 2-->
-               <!-- START: 9 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 3-->
-               <!-- START: 9 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 4-->
-               <!-- START: 9 samples, no refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="hidden"  name="reffile5" value="na"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 5-->
-               <!-- START: 9 samples, no refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="hidden"  name="reffile6" value="na"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 6-->
-               <!-- START: 9 samples, no refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="hidden"  name="reffile7" value="na"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 7-->
-               <!-- START: 9 samples, no refpairs, entry 8-->
-               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
-               <param  type="hidden"  name="reffile8" value="na"/>  
-               <conditional name="genelist8">
-                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist8"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
-               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
-               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 8-->
-               <!-- START: 9 samples, no refpairs, entry 9-->
-               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
-               <param  type="hidden"  name="reffile9" value="na"/>  
-               <conditional name="genelist9">
-                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist9"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
-               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
-               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
-               <!-- END: 9 samples, no refpairs, entry 9-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 9 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 1-->
-               <!-- START: 9 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 2-->
-               <!-- START: 9 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 3-->
-               <!-- START: 9 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 4-->
-               <!-- START: 9 samples, yes refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 5-->
-               <!-- START: 9 samples, yes refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 6-->
-               <!-- START: 9 samples, yes refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 7-->
-               <!-- START: 9 samples, yes refpairs, entry 8-->
-               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
-               <param  type="data"  name="reffile8" label="Sample 8: Reference BAM file"/>  
-               <conditional name="genelist8">
-                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist8"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
-               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
-               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 8-->
-               <!-- START: 9 samples, yes refpairs, entry 9-->
-               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
-               <param  type="data"  name="reffile9" label="Sample 9: Reference BAM file"/>  
-               <conditional name="genelist9">
-                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist9"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
-               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
-               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
-               <!-- END: 9 samples, yes refpairs, entry 9-->
-            </when> 
-         </conditional>
-      </when>                     
-      <when value="10">                     
-         <conditional name="usepair">
-            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
-               <option value="no">No</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="no">                     
-               <!-- START: 10 samples, no refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="hidden"  name="reffile1" value="na"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 1-->
-               <!-- START: 10 samples, no refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="hidden"  name="reffile2" value="na"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 2-->
-               <!-- START: 10 samples, no refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="hidden"  name="reffile3" value="na"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 3-->
-               <!-- START: 10 samples, no refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="hidden"  name="reffile4" value="na"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 4-->
-               <!-- START: 10 samples, no refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="hidden"  name="reffile5" value="na"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 5-->
-               <!-- START: 10 samples, no refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="hidden"  name="reffile6" value="na"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 6-->
-               <!-- START: 10 samples, no refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="hidden"  name="reffile7" value="na"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 7-->
-               <!-- START: 10 samples, no refpairs, entry 8-->
-               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
-               <param  type="hidden"  name="reffile8" value="na"/>  
-               <conditional name="genelist8">
-                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist8"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
-               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
-               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 8-->
-               <!-- START: 10 samples, no refpairs, entry 9-->
-               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
-               <param  type="hidden"  name="reffile9" value="na"/>  
-               <conditional name="genelist9">
-                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist9"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
-               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
-               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 9-->
-               <!-- START: 10 samples, no refpairs, entry 10-->
-               <param  type="data"  name="bamfile10" label="Sample 10: Input BAM file"/>
-               <param  type="hidden"  name="reffile10" value="na"/>  
-               <conditional name="genelist10">
-                  <param type="select" name="usegenelist10" label="Sample 10: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist10"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist10"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title10" value="plot10" label="Sample 10: Image title"/>  
-               <param  type="text"  name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>  
-               <param  type="text"  name="linecol10" value="tan3" label="Sample 10: Line plot color"/>  
-               <!-- END: 10 samples, no refpairs, entry 10-->
-            </when> 
-            <when value="yes">                     
-               <!-- START: 10 samples, yes refpairs, entry 1-->
-               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
-               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
-               <conditional name="genelist1">
-                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist1"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
-               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
-               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 1-->
-               <!-- START: 10 samples, yes refpairs, entry 2-->
-               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
-               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
-               <conditional name="genelist2">
-                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist2"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
-               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
-               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 2-->
-               <!-- START: 10 samples, yes refpairs, entry 3-->
-               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
-               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
-               <conditional name="genelist3">
-                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist3"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
-               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
-               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 3-->
-               <!-- START: 10 samples, yes refpairs, entry 4-->
-               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
-               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
-               <conditional name="genelist4">
-                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist4"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
-               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
-               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 4-->
-               <!-- START: 10 samples, yes refpairs, entry 5-->
-               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
-               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
-               <conditional name="genelist5">
-                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist5"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
-               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
-               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 5-->
-               <!-- START: 10 samples, yes refpairs, entry 6-->
-               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
-               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
-               <conditional name="genelist6">
-                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist6"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
-               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
-               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 6-->
-               <!-- START: 10 samples, yes refpairs, entry 7-->
-               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
-               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
-               <conditional name="genelist7">
-                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist7"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
-               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
-               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 7-->
-               <!-- START: 10 samples, yes refpairs, entry 8-->
-               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
-               <param  type="data"  name="reffile8" label="Sample 8: Reference BAM file"/>  
-               <conditional name="genelist8">
-                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist8"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
-               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
-               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 8-->
-               <!-- START: 10 samples, yes refpairs, entry 9-->
-               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
-               <param  type="data"  name="reffile9" label="Sample 9: Reference BAM file"/>  
-               <conditional name="genelist9">
-                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist9"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
-               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
-               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 9-->
-               <!-- START: 10 samples, yes refpairs, entry 10-->
-               <param  type="data"  name="bamfile10" label="Sample 10: Input BAM file"/>
-               <param  type="data"  name="reffile10" label="Sample 10: Reference BAM file"/>  
-               <conditional name="genelist10">
-                  <param type="select" name="usegenelist10" label="Sample 10: Gene list">
-                     <option value="no">Plot whole genome</option>
-                     <option value="yes">Provide restricted gene list</option>
-                  </param>
-                  <when value="no">                     
-                     <param type="hidden"  name="genelist10"  value="-1"/>
-                  </when>
-                  <when value="yes">
-                     <param type="data"  name="genelist10"  label="Choose the uploaded gene list for plotting"/>
-                  </when>
-               </conditional>
-               <param  type="text"  name="title10" value="plot10" label="Sample 10: Image title"/>  
-               <param  type="text"  name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>  
-               <param  type="text"  name="linecol10" value="tan3" label="Sample 10: Line plot color"/>  
-               <!-- END: 10 samples, yes refpairs, entry 10-->
-            </when> 
-         </conditional>
-      </when>                     
-   </conditional>
-
-
-   
-   <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
-      <option value="ensembl">Ensembl</option>
-      <option value="refseq">RefSeq</option>
-   </param>
-   <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/>
-   <conditional name="GO">
-      <param type="select" name="gene_order" label="Gene order algorithm">
-         <option value="total">Overall enrichment of the 1st profile</option>
-         <option value="hc">Hierarchical clustering</option>
-         <option value="max">Peak value of the 1st profile</option>
-         <option value="prod">Product of all profiles on the same region</option>
-         <option value="diff">Difference between the 1st and 2nd profiles</option>
-         <option value="km">K-means clustering</option>
-         <option value="none">No ranking algorithm applied. Use order in gene list.</option>
-      </param>
-      <when value="km">
-         <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
-         <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
-         <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-      </when>
-      <when value="total">
-         <param type="hidden" name="KNC" value="NA" />
-         <param type="hidden" name="MIT" value="NA" />
-         <param type="hidden" name="NRS" value="NA" />
-      </when>
-      <when value="hc">
-         <param type="hidden" name="KNC" value="NA" />
-         <param type="hidden" name="MIT" value="NA" />
-         <param type="hidden" name="NRS" value="NA" />
-      </when>
-      <when value="max">
-         <param type="hidden" name="KNC" value="NA" />
-         <param type="hidden" name="MIT" value="NA" />
-         <param type="hidden" name="NRS" value="NA" />
-      </when>
-      <when value="prod">
-         <param type="hidden" name="KNC" value="NA" />
-         <param type="hidden" name="MIT" value="NA" />
-         <param type="hidden" name="NRS" value="NA" />
-      </when>
-      <when value="diff">
-         <param type="hidden" name="KNC" value="NA" />
-         <param type="hidden" name="MIT" value="NA" />
-         <param type="hidden" name="NRS" value="NA" />
-      </when>
-      <when value="none">
-         <param type="hidden" name="KNC" value="NA" />
-         <param type="hidden" name="MIT" value="NA" />
-         <param type="hidden" name="NRS" value="NA" />
-      </when>
-   </conditional>
-   <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/>
-   <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/>
-   <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
-      <option value="1">Yes</option>
-      <option value="0">No</option>
-   </param>
-
-   <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/>
-   <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/>
-   <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
-      <option value="1">No</option>
-      <option value="3">Slightly</option>
-      <option value="5">Somewhat</option>
-      <option value="9">Quite</option>
-      <option value="13">Super</option>
-   </param>
-   <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/>
-<!--
--->
-</inputs>
-
-<help>---TEST---</help>
-<outputs>
-   <data format="pdf" name="out_avg_png" />
-   <data format="pdf" name="out_hm_png" />
-   <data format="zip" name="out_zip"/>
-</outputs>
-</tool>
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed/ngsplot_main/runNGSplot.pl
--- a/ngsplot_galaxytoolshed/ngsplot_main/runNGSplot.pl	Wed Mar 18 15:06:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use File::Basename 'dirname';
-use File::Spec;
-use Cwd 'abs_path';
-
-my @inputs = @ARGV;
-my @inputs2 = @inputs;
-
-my $genome_name = shift(@inputs);
-my $genomic_region_source_type__genomic_region = shift(@inputs);
-my $genomic_region_source_type__further_information = shift(@inputs);
-my $genomic_region_source_type__interval_size = shift(@inputs);
-my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_option = shift(@inputs);
-my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size = shift(@inputs);
-my $numsamples = shift(@inputs);
-my $usepairs = shift(@inputs);
-
-#print STDERR "inputs @inputs\n";
-
-my $randfile = rand(100)."\.config\.txt";
-my $randfile2 = $randfile;
-$randfile2 =~ s/config\.txt/logfile/gm;
-
-my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile");
-open(FILE,">$outfile");
-
-for (my $i=1;$i<=$numsamples;$i++) {
-   my $bamfile=shift(@inputs);
-   my $reffile=shift(@inputs);
-   my $usegenelist=shift(@inputs);
-   my $genelist=shift(@inputs);
-   my $title=shift(@inputs);
-   my $fraglen=shift(@inputs);
-   my $color=shift(@inputs);   
-   if ($usepairs eq 'yes') {
-      syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n");
-   }else {
-      syswrite(FILE, "$bamfile\t$genelist\t$title\t$fraglen\t$color\n");
-   }
-}
-close(FILE);
-
-my $gene_database = shift(@inputs);
-my $randomly_sample = shift(@inputs);
-my $gene_order = shift(@inputs);
-my $knc = shift(@inputs);
-my $mit = shift(@inputs);
-my $nrs = shift(@inputs);
-my $chunk_size = shift(@inputs);
-my $quality_requirement = shift(@inputs);
-my $standard_error = shift(@inputs);
-my $radius_size = shift(@inputs);
-my $flooding_fraction = shift(@inputs);
-my $smooth_method = shift(@inputs);
-my $shaded_area = shift(@inputs);
-my $out_name = shift(@inputs);
-my $out_avg_name = shift(@inputs);
-my $out_hm_name = shift(@inputs);
-
-
-my $G = $genome_name;
-my $R = $genomic_region_source_type__genomic_region;
-my $C = $outfile;
-my $O = $out_name;
-my $O2 = $out_avg_name;
-my $O3 = $out_hm_name;
-my $F = $genomic_region_source_type__further_information;
-my $D = $gene_database;
-my $L = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
-my $N = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
-my $RB = $radius_size;
-my $S = $randomly_sample;
-my $CS = $chunk_size;
-my $MQ = $quality_requirement;
-my $IN = $genomic_region_source_type__interval_size;
-my $SE = $standard_error;
-my $MW = $smooth_method;
-my $H = $shaded_area;
-my $GO = $gene_order;
-my $KNC = $knc;
-my $MIT = $mit;
-my $NRS = $nrs;
-my $FC = $flooding_fraction;
-
-if ($GO eq 'km') {
-   $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS";
-}
-
-my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2");
-open(FILE2,">>$logfile");
-my $cmd5="pwd >> $logfile 2>&1";
-system($cmd5);
-
-my $cmd='';
-if (($R eq 'tss')||($R eq 'tes')) {
-   $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
-}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') {
-   if ($IN eq 'automatic') {
-      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
-   }else {
-      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN  >> $logfile 2>&1";
-   }
-}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') {
-   if ($IN eq 'automatic') {
-      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H  >> $logfile 2>&1";
-   }else {
-      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN  >> $logfile 2>&1";
-   }
-}
-my $cmd2="cp data.zip $O";
-my $cmd3="rm $outfile";
-my $cmd4="rm $logfile";
-syswrite(FILE2, "\n$cmd\n");
-syswrite(FILE2, "\n$cmd2\n");
-syswrite(FILE2, "\n$cmd3\n");
-syswrite(FILE2, "\n$cmd4\n\n");
-
-system($cmd);
-system($cmd2);
-system($cmd3);
-system($cmd4);
-
-close(FILE2);
-
-
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed/ngsplot_replot/replot.xml
--- a/ngsplot_galaxytoolshed/ngsplot_replot/replot.xml	Wed Mar 18 15:06:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,157 +0,0 @@
-<tool id="replot" name="replot">
-<command interpreter="perl">
-#if $outtype.outtype2 == "prof":
-   runreplot.pl $input_zipfile $outtype.outtype2 $output_filename 
-   $outtype.WD
-   $outtype.HG
-   $outtype.SE
-   $outtype.H
-   $outtype.MW
-   $outtype.Y.Y2
-   $outtype.Y.Y3
-   $outtype.LEG
-   $outtype.BOX
-   $outtype.VLN
-   $outtype.XYL
-   $outtype.LWD
-   $outtype.FS
-#else if $outtype.outtype2 == "heatmap":
-   runreplot.pl $input_zipfile $outtype.outtype2 $output_filename 
-   $outtype.GO.GO2
-   $outtype.GO.KNC
-   $outtype.GO.MIT
-   $outtype.GO.NRS
-   $outtype.LOW
-   $outtype.RR
-   $outtype.FC
-   $outtype.CO
-   $outtype.CD
-   $outtype.FS
-   dummy
-   dummy
-   dummy
-#end if:
-
-</command>
-
-<!-->
-
-
-<-->
-
-<inputs>
-   <param  type="data"  name="input_zipfile" multiple="false" label="Input zip file created by ngsplot"/>
-
-   <conditional name="outtype">
-      <param  type="select"  name="outtype2" label="Select figure type to replot">
-         <option value="prof">Coverage Profile</option>
-         <option value="heatmap">Heatmap</option>
-      </param>
-
-      <when value="prof">
-         <param type="text" name="WD" value="8" label="Image width in inches" />
-         <param type="text" name="HG" value="7" label="Image height in inches" />
-         <param type="select" name="SE" label="Standard error shading" >
-            <option value="1">Yes, include standard error shading</option>
-            <option value="0">No, exclude standard error shading</option>
-         </param>
-         <param type="text" name="H" value="0" label="Opacity of shaded area under each curve" help="Use 0 for no shading. Suggested value of between 0 and 0.5 will add a semi-transparent shade under each curve."/>
-         <param type="text" name="MW" value="1" label="Moving window width to smooth average profiles" help="The unit of the window size is a data point. In ngs.plot, the number of data points on the X-axis is 100. A moving window width of 10 means averaging over 10% of the entire X-axis."/>
-         <conditional name="Y">
-            <param type="select" name="Y2" label="Define Y-axis scale?" >
-               <option value="no">No, let program decide</option>
-               <option value="yes">Yes</option>
-            </param>
-            <when value="yes">
-               <param type="text" name="Y3" value="0,100" label="Y-axis min_val,max_val" help="Enter minimum and maximum value separated by comma" />
-            </when>
-            <when value="no">
-               <param type="hidden" name="Y3" value="na" label="test"/>
-            </when>
-         </conditional>
-         <param type="select" name="LEG" label="Draw legend?" >
-            <option value="1">Yes</option>
-            <option value="0">No</option>
-         </param>
-         <param type="select" name="BOX" label="Draw box around plot?" >
-            <option value="1">Yes</option>
-            <option value="0">No</option>
-         </param>
-         <param type="select" name="VLN" label="Draw vertical lines?" >
-            <option value="1">Yes</option>
-            <option value="0">No</option>
-         </param>
-         <param type="select" name="XYL" label="Draw axis labels?" >
-            <option value="1">Yes</option>
-            <option value="0">No</option>
-         </param>
-         <param type="text" name="LWD" value="3" label="Line width" />
-         <param type="text" name="FS" value="12" label="Font size" />
-<!-->
-<-->
-
-      </when>
-      <when value="heatmap">
-         <conditional name="GO">
-            <param type="select" name="GO2" label="Gene order algorithm" >
-               <option value="total">Overall enrichment of the 1st profile (default)</option>
-               <option value="hc">Hierarchial clustering</option>
-               <option value="max">Peak value of the 1st profile</option>
-               <option value="prod">Product of all profiles on the same region</option>
-               <option value="diff">Difference between 1st and 2nd profiles</option>
-               <option value="km">K-means clustering.</option>
-               <option value="none">No ranking algorithm applied, use order in gene list.</option>
-            </param>
-            <when value="km">
-               <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
-               <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
-               <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-            <when value="total">
-               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
-               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
-               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-            <when value="hc">
-               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
-               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
-               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-            <when value="max">
-               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
-               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
-               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-            <when value="prod">
-               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
-               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
-               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-            <when value="diff">
-               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
-               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
-               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-            <when value="none">
-               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
-               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
-               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
-            </when> 
-         </conditional>
-         <param type="text" name="LOW" value="10" label="Low count cutoff in rank-based normalization" help="This number is in raw read counts."/>
-         <param type="text" name="RR" value="30" label="Reduce ratio" help="This controls the heatmap height. The smaller the value, the taller the heatmap." />
-         <param type="text" name="FC" value="0.02" label="Flooding fraction" help="The default value of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic." />
-         <param type="text" name="CO" value="default" label="Color for heatmap" help="For non bam-pair plots, input a single color. For bam-pair plots, use color-tri format (neg_color:[neu_color]:pos_color). Hint: must use R colors, such as darkgreen, yellow and blue2. The neutral color is optional(default=black)." />
-         <param type="text" name="CD" value="0.6" label="Color distribution for heatmap" help="Must be a positive number. Hint: lower values give more widely spaced colors at the negative end. In other words, they shift the neutral color to positive values. If set to 1, the neutral color represents 0(i.e. no bias). If set to >1, the neutral color represents a negative value." />
-         <param type="text" name="FS" value="12" label="Font size" />
-      </when>
-   </conditional>
-<!--
--->
-</inputs>
-
-<help>---TEST---</help>
-<outputs>
-   <data format="pdf" name="output_filename" />
-</outputs>
-</tool>
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed/ngsplot_replot/runreplot.pl
--- a/ngsplot_galaxytoolshed/ngsplot_replot/runreplot.pl	Wed Mar 18 15:06:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,63 +0,0 @@
-#!/usr/bin/perl -w
-use strict;
-use File::Basename 'dirname';
-use File::Spec;
-use Cwd 'abs_path';
-
-my $input_file = $ARGV[0];
-my $output_type = $ARGV[1];
-my $output_filename = $ARGV[2];
-
-my $cmd1 = "cp $input_file data.zip";
-my $cmd2 = "";
-my $cmd3 = "mv output.pdf $output_filename";
-
-my $FS = "";
-if ($output_type eq 'prof') {
-   my $WD = "-WD $ARGV[3]";
-   my $HG = "-HG $ARGV[4]";
-   my $SE = "-SE $ARGV[5]";
-   my $H = "-H $ARGV[6]";
-   my $MW = "-MW $ARGV[7]";
-   my $Y = "-Y $ARGV[8]";
-   my $YAS = "-YAS $ARGV[9]";
-   my $LEG = "-LEG $ARGV[10]";
-   my $BOX = "-BOX $ARGV[11]";
-   my $VLN = "-VLN $ARGV[12]";
-   my $XYL = "-XYL $ARGV[13]";
-   my $LWD = "-LWD $ARGV[14]";
-   $FS = "-FS $ARGV[15]";
-
-   if ($Y =~ /no$/gm) {
-      $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS";
-   }else {
-      $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS $YAS";
-   }
-}elsif ($output_type eq 'heatmap') {
-   my $GO = "-GO $ARGV[3]";
-   my $KNC = "-KNC $ARGV[4]";
-   my $MIT = "-MIT $ARGV[5]";
-   my $NRS = "-NRS $ARGV[6]";
-   my $LOW = "-LOW $ARGV[7]";
-   my $RR = "-RR $ARGV[8]";
-   my $FC = "-FC $ARGV[9]";
-   my $CO = "-CO $ARGV[10]";
-   my $CD = "-CD $ARGV[11]";
-   $FS = "-FS $ARGV[12]";
-   my $DUM1 = $ARGV[13];
-   my $DUM2 = $ARGV[14];
-   my $DUM3 = $ARGV[15];
-
-   if ($CO =~ /default/gm) { $CO = ""; }
-
-   if ($GO =~ /km$/gm) {
-      $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO $KNC $MIT $NRS"; 
-   }else {
-      $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO";
-   }
-}
-system($cmd1);
-system($cmd2);
-system($cmd3);
-
-
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/.tool_dependencies.xml.swp
Binary file ngsplot_galaxytoolshed_v1.0/.tool_dependencies.xml.swp has changed
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/ngsplot-2.47.1.tar.gz
Binary file ngsplot_galaxytoolshed_v1.0/ngsplot-2.47.1.tar.gz has changed
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/ngsplot_intro/intro.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v1.0/ngsplot_intro/intro.xml	Wed Mar 18 15:43:54 2015 -0400
@@ -0,0 +1,67 @@
+<tool id="ngs.plot_intro" name="Introduction">
+<command interpreter="perl">
+
+</command>
+
+#if $numsamples.numsamples2 == "1":
+   runNGSplot.pl 
+   $genome_name 
+
+#else if $numsamples.numsamples2 == "5":
+   runNGSplot.pl 
+   $genome_name 
+
+#end if:
+
+<!--
+<inputs>
+   <param  type="text" value="mm9" name="genome_name" label="Intro Text here..." help="" >
+   </param>
+</inputs>
+-->
+
+<help>
+
+**WELCOME TO NGS.PLOT ON GALAXY**
+
+-----
+
+**HOW TO USE**
+
+To use ngs.plot here on this GUI-based galaxy implementation, first upload your alignment BAM file(s) using the *Get Data* -> **Upload File** tool on top of the left panel of this page. The names of your uploaded file(s) will then be displayed on the right panel. Next, select the *NGS.PLOT V2.47.1* -> **ngs.plot** tool on the left panel and all other input information required from you will be displayed as a form on the main central panel. Complete the form then click the *Execute* button to launch the program. Three output files (a profile chart, a heatmap, and a zipped data file) will be generated and displayed on the right panel, which you can click on to view. To further replot the figures into a format that you desire, use the *NGS.PLOT V2.47.1* -> **replot** tool with it's input file being the zip file previously generated by 'ngs.plot'.
+
+For a more detailed explanation of how to run ngs.plot on Galaxy, please see the tutorial at https://code.google.com/p/ngsplot/wiki/webngsplot. 
+
+-----
+
+**INTRODUCTION**
+
+ngs.plot is a program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
+
+DNA sequencing is at the core of genomics. The NGS technology has been tremendously improved in the past few years. It can now determine more than a billion DNA sequences within a week, generating terabytes of data. Applications include but are not limited to: 1. ChIP-seq which profiles genome-wide protein-DNA interactions; 2. RNA-seq which measures the gene expression levels. It is very helpful to look at the enrichment of those sequences at various functional regions. Although a genome browser (such as the UCSC genome browser) allows a researcher to visualize these data, it limits the view to a slice of the genome. While the genome is like a huge collection of functional elements that can be classified into different categories. Each category of elements may perform distinct functions and they might further contain modules.
+
+The signature advantage of ngs.plot is that it collects a large database of functional elements for many genomes. A user can ask for a functionally important region to be displayed in one command. It handles large sequencing data efficiently and has only modest memory requirement. For example, ngs.plot was used to draw a plot for all the genes on the mouse genome from 71GB of ChIP-seq data in 25 min, with a memory footprint of 2.7GB using 4 x 2.4GHz CPU cores. ngs.plot is also easy to use. A user only needs to create a very small text file called configuration, telling the program which samples to look at and how they should be combined with different regions, and then run the program with one command. This Galaxy web-based version of ngs.plot is also available for users not familiar with command-line programs. For additional program details, please refer to our project homepage at https://code.google.com/p/ngsplot or to the publication cited below. 
+
+-----
+
+**COMMERCIAL USE**
+
+ngs.plot is free for use by academic users. If you want to use it in commercial settings, please contact Lisa Placanica at: lisa.placanica@mssm.edu
+
+**HOW TO CITE**
+
+Shen, L.*, Shao, N., Liu, X. and Nestler, E. (2014) ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases, BMC Genomics, 15, 284.
+
+**CONTACT**
+
+ngs.plot is developed by Drs. Li Shen, Ningyi Shao and Xiaochuan Liu at the Icahn School of Medicine at Mount Sinai. If you have technical questions about ngs.plot, please use the discussion forum. For collaborations or any other matters, use: li.shen AT mssm.edu.
+
+</help>
+<outputs>
+<!--
+   <data format="pdf" name="out_avg_png" />
+   <data format="pdf" name="out_hm_png" />
+   <data format="zip" name="out_zip"/>
+-->
+</outputs>
+</tool>
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/ngsplot_main/ngsplot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v1.0/ngsplot_main/ngsplot.xml	Wed Mar 18 15:43:54 2015 -0400
@@ -0,0 +1,3179 @@
+<tool id="ngs.plot" name="ngs.plot">
+
+<requirements>
+    <requirement type="package" version="2.47.1">ngsplot</requirement>
+</requirements>
+
+<command interpreter="perl">
+#if $numsamples.numsamples2 == "1":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "2":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "3":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "4":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+   
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "5":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+
+   $numsamples.usepair.bamfile5
+   $numsamples.usepair.reffile5
+   $numsamples.usepair.genelist5.usegenelist5
+   $numsamples.usepair.genelist5.genelist5
+   $numsamples.usepair.title5
+   $numsamples.usepair.fraglen5
+   $numsamples.usepair.linecol5
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "6":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+
+   $numsamples.usepair.bamfile5
+   $numsamples.usepair.reffile5
+   $numsamples.usepair.genelist5.usegenelist5
+   $numsamples.usepair.genelist5.genelist5
+   $numsamples.usepair.title5
+   $numsamples.usepair.fraglen5
+   $numsamples.usepair.linecol5
+
+   $numsamples.usepair.bamfile6
+   $numsamples.usepair.reffile6
+   $numsamples.usepair.genelist6.usegenelist6
+   $numsamples.usepair.genelist6.genelist6
+   $numsamples.usepair.title6
+   $numsamples.usepair.fraglen6
+   $numsamples.usepair.linecol6
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "7":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+
+   $numsamples.usepair.bamfile5
+   $numsamples.usepair.reffile5
+   $numsamples.usepair.genelist5.usegenelist5
+   $numsamples.usepair.genelist5.genelist5
+   $numsamples.usepair.title5
+   $numsamples.usepair.fraglen5
+   $numsamples.usepair.linecol5
+
+   $numsamples.usepair.bamfile6
+   $numsamples.usepair.reffile6
+   $numsamples.usepair.genelist6.usegenelist6
+   $numsamples.usepair.genelist6.genelist6
+   $numsamples.usepair.title6
+   $numsamples.usepair.fraglen6
+   $numsamples.usepair.linecol6
+
+   $numsamples.usepair.bamfile7
+   $numsamples.usepair.reffile7
+   $numsamples.usepair.genelist7.usegenelist7
+   $numsamples.usepair.genelist7.genelist7
+   $numsamples.usepair.title7
+   $numsamples.usepair.fraglen7
+   $numsamples.usepair.linecol7
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "8":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+
+   $numsamples.usepair.bamfile5
+   $numsamples.usepair.reffile5
+   $numsamples.usepair.genelist5.usegenelist5
+   $numsamples.usepair.genelist5.genelist5
+   $numsamples.usepair.title5
+   $numsamples.usepair.fraglen5
+   $numsamples.usepair.linecol5
+
+   $numsamples.usepair.bamfile6
+   $numsamples.usepair.reffile6
+   $numsamples.usepair.genelist6.usegenelist6
+   $numsamples.usepair.genelist6.genelist6
+   $numsamples.usepair.title6
+   $numsamples.usepair.fraglen6
+   $numsamples.usepair.linecol6
+
+   $numsamples.usepair.bamfile7
+   $numsamples.usepair.reffile7
+   $numsamples.usepair.genelist7.usegenelist7
+   $numsamples.usepair.genelist7.genelist7
+   $numsamples.usepair.title7
+   $numsamples.usepair.fraglen7
+   $numsamples.usepair.linecol7
+
+   $numsamples.usepair.bamfile8
+   $numsamples.usepair.reffile8
+   $numsamples.usepair.genelist8.usegenelist8
+   $numsamples.usepair.genelist8.genelist8
+   $numsamples.usepair.title8
+   $numsamples.usepair.fraglen8
+   $numsamples.usepair.linecol8
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "9":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+
+   $numsamples.usepair.bamfile5
+   $numsamples.usepair.reffile5
+   $numsamples.usepair.genelist5.usegenelist5
+   $numsamples.usepair.genelist5.genelist5
+   $numsamples.usepair.title5
+   $numsamples.usepair.fraglen5
+   $numsamples.usepair.linecol5
+
+   $numsamples.usepair.bamfile6
+   $numsamples.usepair.reffile6
+   $numsamples.usepair.genelist6.usegenelist6
+   $numsamples.usepair.genelist6.genelist6
+   $numsamples.usepair.title6
+   $numsamples.usepair.fraglen6
+   $numsamples.usepair.linecol6
+
+   $numsamples.usepair.bamfile7
+   $numsamples.usepair.reffile7
+   $numsamples.usepair.genelist7.usegenelist7
+   $numsamples.usepair.genelist7.genelist7
+   $numsamples.usepair.title7
+   $numsamples.usepair.fraglen7
+   $numsamples.usepair.linecol7
+
+   $numsamples.usepair.bamfile8
+   $numsamples.usepair.reffile8
+   $numsamples.usepair.genelist8.usegenelist8
+   $numsamples.usepair.genelist8.genelist8
+   $numsamples.usepair.title8
+   $numsamples.usepair.fraglen8
+   $numsamples.usepair.linecol8
+
+   $numsamples.usepair.bamfile9
+   $numsamples.usepair.reffile9
+   $numsamples.usepair.genelist9.usegenelist9
+   $numsamples.usepair.genelist9.genelist9
+   $numsamples.usepair.title9
+   $numsamples.usepair.fraglen9
+   $numsamples.usepair.linecol9
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#else if $numsamples.numsamples2 == "10":
+   runNGSplot.pl 
+   $genome_name 
+   $genomic_region_source_type.genomic_region 
+   $genomic_region_source_type.further_information 
+   $genomic_region_source_type.interval_size 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_option 
+   $genomic_region_source_type.flanking_region_option_source_type.flanking_region_size 
+   $numsamples.numsamples2
+   $numsamples.usepair.usepair1
+
+   $numsamples.usepair.bamfile1
+   $numsamples.usepair.reffile1
+   $numsamples.usepair.genelist1.usegenelist1
+   $numsamples.usepair.genelist1.genelist1
+   $numsamples.usepair.title1
+   $numsamples.usepair.fraglen1
+   $numsamples.usepair.linecol1
+
+   $numsamples.usepair.bamfile2
+   $numsamples.usepair.reffile2
+   $numsamples.usepair.genelist2.usegenelist2
+   $numsamples.usepair.genelist2.genelist2
+   $numsamples.usepair.title2
+   $numsamples.usepair.fraglen2
+   $numsamples.usepair.linecol2
+
+   $numsamples.usepair.bamfile3
+   $numsamples.usepair.reffile3
+   $numsamples.usepair.genelist3.usegenelist3
+   $numsamples.usepair.genelist3.genelist3
+   $numsamples.usepair.title3
+   $numsamples.usepair.fraglen3
+   $numsamples.usepair.linecol3
+
+   $numsamples.usepair.bamfile4
+   $numsamples.usepair.reffile4
+   $numsamples.usepair.genelist4.usegenelist4
+   $numsamples.usepair.genelist4.genelist4
+   $numsamples.usepair.title4
+   $numsamples.usepair.fraglen4
+   $numsamples.usepair.linecol4
+
+   $numsamples.usepair.bamfile5
+   $numsamples.usepair.reffile5
+   $numsamples.usepair.genelist5.usegenelist5
+   $numsamples.usepair.genelist5.genelist5
+   $numsamples.usepair.title5
+   $numsamples.usepair.fraglen5
+   $numsamples.usepair.linecol5
+
+   $numsamples.usepair.bamfile6
+   $numsamples.usepair.reffile6
+   $numsamples.usepair.genelist6.usegenelist6
+   $numsamples.usepair.genelist6.genelist6
+   $numsamples.usepair.title6
+   $numsamples.usepair.fraglen6
+   $numsamples.usepair.linecol6
+
+   $numsamples.usepair.bamfile7
+   $numsamples.usepair.reffile7
+   $numsamples.usepair.genelist7.usegenelist7
+   $numsamples.usepair.genelist7.genelist7
+   $numsamples.usepair.title7
+   $numsamples.usepair.fraglen7
+   $numsamples.usepair.linecol7
+
+   $numsamples.usepair.bamfile8
+   $numsamples.usepair.reffile8
+   $numsamples.usepair.genelist8.usegenelist8
+   $numsamples.usepair.genelist8.genelist8
+   $numsamples.usepair.title8
+   $numsamples.usepair.fraglen8
+   $numsamples.usepair.linecol8
+
+   $numsamples.usepair.bamfile9
+   $numsamples.usepair.reffile9
+   $numsamples.usepair.genelist9.usegenelist9
+   $numsamples.usepair.genelist9.genelist9
+   $numsamples.usepair.title9
+   $numsamples.usepair.fraglen9
+   $numsamples.usepair.linecol9
+
+   $numsamples.usepair.bamfile10
+   $numsamples.usepair.reffile10
+   $numsamples.usepair.genelist10.usegenelist10
+   $numsamples.usepair.genelist10.genelist10
+   $numsamples.usepair.title10
+   $numsamples.usepair.fraglen10
+   $numsamples.usepair.linecol10
+
+   $gene_database
+   $randomly_sample
+   $GO.gene_order
+   $GO.KNC
+   $GO.MIT
+   $GO.NRS
+   $chunk_size
+   $quality_requirement
+   $standard_error
+   $radius_size
+   $flooding_fraction
+   $smooth_method
+   $shaded_area
+   $out_zip  $out_avg_png  $out_hm_png
+
+#end if:
+
+</command>
+
+<!-->
+<-->
+
+<inputs>
+   <param  type="text" value="mm9" name="genome_name" label="Genome" help="(hg19, mm9, rn4, or other genomes supported by your NGS.plot installation)" >
+   </param>
+   <conditional name="genomic_region_source_type">
+      <param type="select" name="genomic_region" label="Genomic region" help="">
+         <option value="tss">TSS</option>
+         <option value="tes">TES</option>
+         <option value="genebody">Genebody</option>
+         <option value="exon">Exon</option>
+         <option value="cgi">CGI</option>
+         <option value="bed">Customized bed file</option>
+      </param>
+
+      <when value="tss"> 
+         <param type="select" name="further_information"  label="Further information: Not required for TSS">
+            <option value="na">Not Required</option>
+         </param>
+         <param name="interval_size" type="select" label="Interval Region Size: Not required for TSS">
+            <option value="na">Not Required</option>
+         </param>
+         <conditional name="flanking_region_option_source_type">
+            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
+               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
+               <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
+            </param>
+            <when value="flanking_region_size">
+               <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
+            </when>
+            <!--when value="flanking_floating_size">
+               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
+            </when-->
+         </conditional>
+      </when> 
+      <when value="tes"> 
+         <param type="select" name="further_information"  label="Further information: Not required for TES">
+            <option value="na">Not Required</option>
+         </param>
+         <param name="interval_size" type="select" label="Interval Region Size: Not required for TES">
+            <option value="na">Not Required</option>
+         </param>
+         <conditional name="flanking_region_option_source_type">
+            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
+               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
+               <!--option value="flanking_floating_size">Specify fractional size with respect to interval size</option-->
+            </param>
+            <when value="flanking_region_size">
+               <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
+            </when>
+            <!--when value="flanking_floating_size">
+               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
+            </when-->
+         </conditional>
+      </when> 
+      <when value="genebody"> 
+         <param type="select" name="further_information"  label="You selected Genebody, further information can be provided for specific regions to plot">
+            <option value="chipseq">ChIP-seq</option>
+            <option value="rnaseq">RNA-seq</option>
+         </param>
+         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
+            <option value="automatic">Default</option>
+            <option value="0">Small</option>
+            <option value="1">Large</option>
+         </param>
+         <conditional name="flanking_region_option_source_type">
+            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
+               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
+               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
+            </param>
+            <when value="flanking_region_size">
+               <param name="flanking_region_size" size="30" type="text" value="2000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
+            </when>
+            <when value="flanking_floating_size">
+               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
+            </when>
+         </conditional>            
+      </when>
+      <when value="exon"> 
+         <param type="select" name="further_information"  label="You selected Exon, further information can be provided for specific regions to plot">
+            <option value="canonical">Canonical</option>
+            <option value="variant">Variant</option>
+            <option value="promoter">Promoter</option>
+            <option value="polyA">polyA</option>
+            <option value="altAcceptor">altAcceptor</option>
+            <option value="altDonor">altDonor</option>
+            <option value="altBoth">altBoth</option>
+         </param>
+         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
+            <option value="automatic">Default</option>
+            <option value="0">Small</option>
+            <option value="1">Large</option>
+         </param>
+         <conditional name="flanking_region_option_source_type">
+            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
+               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
+               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
+            </param>
+            <when value="flanking_region_size">
+               <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
+            </when>
+            <when value="flanking_floating_size">
+               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>
+            </when>
+         </conditional>
+      </when>
+      <when value="cgi"> 
+         <param type="select" name="further_information"  label="You select CGI, further information can be provided for specific regions to plot">
+            <option value="ProximalPromoter">ProximalPromoter</option>
+            <option value="Genebody">GeneBody</option>
+            <option value="Genedesert">GeneDesert</option>
+            <option value="OtherIntergenic">OtherIntergenic</option>
+            <option value="Pericentromere">Pericentromere</option>
+            <option value="Subtelomere">Subtelomere</option>
+            <option value="Promoter1k">Promoter1k</option>
+            <option value="Promoter3k">Promoter3k</option>
+         </param>
+         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
+            <option value="automatic">Default</option>
+            <option value="0">Small</option>
+            <option value="1">Large</option>
+         </param>
+         <conditional name="flanking_region_option_source_type">
+            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
+               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
+               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
+            </param>
+            <when value="flanking_region_size">
+               <param name="flanking_region_size" size="30" type="text" value="500" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
+            </when>
+            <when value="flanking_floating_size">
+               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
+            </when>
+         </conditional>
+      </when> 
+      <when value="bed"> 
+         <param type="select" name="further_information"  label="Further information: Not required for bed input">
+            <option value="na">Not Required</option>
+         </param>
+         <param name="interval_size" type="select" label="Interval Region Size" help="By default, Exon and CGI are small interval; Genebody and bed files are large interval. The X-axis of the plot is separated into 5 equal sized parts. If large interval is chosen, the middle 3 parts are for interval region and the 1 part on each side is for flanking region. If small interval is chosen, the middle 1 part is for interval region and the 2 parts on each side is for flanking region.">
+            <option value="automatic">Default</option>
+            <option value="0">Small</option>
+            <option value="1">Large</option>
+         </param>
+         <conditional name="flanking_region_option_source_type">
+            <param type="select" name="flanking_region_option" label="Choose one method below to plot flanking region">
+               <option value="flanking_region_size">Specify flanking region size in base pairs</option>
+               <option value="flanking_floating_size">Specify fractional size with respect to interval size</option>
+            </param>
+            <when value="flanking_region_size">
+               <param name="flanking_region_size" size="30" type="text" value="1000" label="Flanking region size" help="default varies by type: TSS=2000;TES=2000;Genebody=2000;Exon=500;CGI=500;Bed=1000"/>
+            </when>
+            <when value="flanking_floating_size">
+               <param name="flanking_region_size" size="30" type="text" value="0.33" label="Flanking region size as a fraction (or multiple) of interval size"/>  
+            </when>
+         </conditional>
+      </when> 
+   </conditional>
+
+
+   <conditional name="numsamples">
+      <param type="select" name="numsamples2" label="Number of samples to plot">
+         <option value="1">1</option>
+         <option value="2">2</option>
+         <option value="3">3</option>
+         <option value="4">4</option>
+         <option value="5">5</option>
+         <option value="6">6</option>
+         <option value="7">7</option>
+         <option value="8">8</option>
+         <option value="9">9</option>
+         <option value="10">10</option>
+      </param>
+
+      <when value="1">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 1 sample, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 1 sample, no refpairs, entry 1-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 1 sample, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 1 sample, yes refpairs, entry 1-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="2">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 2 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 2 samples, no refpairs, entry 1-->
+               <!-- START: 2 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 2 samples, no refpairs, entry 2-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 2 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 2 samples, yes refpairs, entry 1-->
+               <!-- START: 2 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 2 samples, yes refpairs, entry 2-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="3">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 3 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 3 samples, no refpairs, entry 1-->
+               <!-- START: 3 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 3 samples, no refpairs, entry 2-->
+               <!-- START: 3 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 3 samples, no refpairs, entry 3-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 3 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 3 samples, yes refpairs, entry 1-->
+               <!-- START: 3 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 3 samples, yes refpairs, entry 2-->
+               <!-- START: 3 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 3 samples, yes refpairs, entry 2-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="4">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 4 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 4 samples, no refpairs, entry 1-->
+               <!-- START: 4 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 4 samples, no refpairs, entry 2-->
+               <!-- START: 4 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 4 samples, no refpairs, entry 3-->
+               <!-- START: 4 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 4 samples, no refpairs, entry 4-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 4 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 4 samples, yes refpairs, entry 1-->
+               <!-- START: 4 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 4 samples, yes refpairs, entry 2-->
+               <!-- START: 4 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 4 samples, yes refpairs, entry 3-->
+               <!-- START: 4 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 4 samples, yes refpairs, entry 4-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="5">           
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 5 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 5 samples, no refpairs, entry 1-->
+               <!-- START: 5 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 5 samples, no refpairs, entry 2-->
+               <!-- START: 5 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 5 samples, no refpairs, entry 3-->
+               <!-- START: 5 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 5 samples, no refpairs, entry 4-->
+               <!-- START: 5 samples, no refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="hidden"  name="reffile5" value="na"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 5 samples, no refpairs, entry 5-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 5 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 5 samples, yes refpairs, entry 1-->
+               <!-- START: 5 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 5 samples, yes refpairs, entry 2-->
+               <!-- START: 5 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 5 samples, yes refpairs, entry 3-->
+               <!-- START: 5 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 5 samples, yes refpairs, entry 4-->
+               <!-- START: 5 samples, yes refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 5 samples, yes refpairs, entry 5-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="6">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?"  help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 6 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 6 samples, no refpairs, entry 1-->
+               <!-- START: 6 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 6 samples, no refpairs, entry 2-->
+               <!-- START: 6 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 6 samples, no refpairs, entry 3-->
+               <!-- START: 6 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 6 samples, no refpairs, entry 4-->
+               <!-- START: 6 samples, no refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="hidden"  name="reffile5" value="na"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 6 samples, no refpairs, entry 5-->
+               <!-- START: 6 samples, no refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="hidden"  name="reffile6" value="na"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 6 samples, no refpairs, entry 6-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 6 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 6 samples, yes refpairs, entry 1-->
+               <!-- START: 6 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 6 samples, yes refpairs, entry 2-->
+               <!-- START: 6 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 6 samples, yes refpairs, entry 3-->
+               <!-- START: 6 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 6 samples, yes refpairs, entry 4-->
+               <!-- START: 6 samples, yes refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 6 samples, yes refpairs, entry 5-->
+               <!-- START: 6 samples, yes refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 6 samples, yes refpairs, entry 6-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="7">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 7 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 1-->
+               <!-- START: 7 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 2-->
+               <!-- START: 7 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 3-->
+               <!-- START: 7 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 4-->
+               <!-- START: 7 samples, no refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="hidden"  name="reffile5" value="na"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 5-->
+               <!-- START: 7 samples, no refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="hidden"  name="reffile6" value="na"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 6-->
+               <!-- START: 7 samples, no refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="hidden"  name="reffile7" value="na"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 7 samples, no refpairs, entry 7-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 7 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 1-->
+               <!-- START: 7 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 2-->
+               <!-- START: 7 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 3-->
+               <!-- START: 7 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 4-->
+               <!-- START: 7 samples, yes refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 5-->
+               <!-- START: 7 samples, yes refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 6-->
+               <!-- START: 7 samples, yes refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 7 samples, yes refpairs, entry 7-->
+            </when> 
+         </conditional>
+     </when>                     
+      <when value="8">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 8 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 1-->
+               <!-- START: 8 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 2-->
+               <!-- START: 8 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 3-->
+               <!-- START: 8 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 4-->
+               <!-- START: 8 samples, no refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="hidden"  name="reffile5" value="na"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 5-->
+               <!-- START: 8 samples, no refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="hidden"  name="reffile6" value="na"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 6-->
+               <!-- START: 8 samples, no refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="hidden"  name="reffile7" value="na"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 7-->
+               <!-- START: 8 samples, no refpairs, entry 8-->
+               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
+               <param  type="hidden"  name="reffile8" value="na"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist8"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
+               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
+               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
+               <!-- END: 8 samples, no refpairs, entry 8-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 8 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 1-->
+               <!-- START: 8 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 2-->
+               <!-- START: 8 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 3-->
+               <!-- START: 8 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 4-->
+               <!-- START: 8 samples, yes refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 5-->
+               <!-- START: 8 samples, yes refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 6-->
+               <!-- START: 8 samples, yes refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 7-->
+               <!-- START: 8 samples, yes refpairs, entry 8-->
+               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
+               <param  type="data"  name="reffile8" label="Sample 8: Reference BAM file"/>  
+               <conditional name="genelist8">
+                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist8"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
+               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
+               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
+               <!-- END: 8 samples, yes refpairs, entry 8-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="9">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 9 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 1-->
+               <!-- START: 9 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 2-->
+               <!-- START: 9 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 3-->
+               <!-- START: 9 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 4-->
+               <!-- START: 9 samples, no refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="hidden"  name="reffile5" value="na"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 5-->
+               <!-- START: 9 samples, no refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="hidden"  name="reffile6" value="na"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 6-->
+               <!-- START: 9 samples, no refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="hidden"  name="reffile7" value="na"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 7-->
+               <!-- START: 9 samples, no refpairs, entry 8-->
+               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
+               <param  type="hidden"  name="reffile8" value="na"/>  
+               <conditional name="genelist8">
+                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist8"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
+               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
+               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 8-->
+               <!-- START: 9 samples, no refpairs, entry 9-->
+               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
+               <param  type="hidden"  name="reffile9" value="na"/>  
+               <conditional name="genelist9">
+                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist9"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
+               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
+               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
+               <!-- END: 9 samples, no refpairs, entry 9-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 9 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 1-->
+               <!-- START: 9 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 2-->
+               <!-- START: 9 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 3-->
+               <!-- START: 9 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 4-->
+               <!-- START: 9 samples, yes refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 5-->
+               <!-- START: 9 samples, yes refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 6-->
+               <!-- START: 9 samples, yes refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 7-->
+               <!-- START: 9 samples, yes refpairs, entry 8-->
+               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
+               <param  type="data"  name="reffile8" label="Sample 8: Reference BAM file"/>  
+               <conditional name="genelist8">
+                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist8"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
+               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
+               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 8-->
+               <!-- START: 9 samples, yes refpairs, entry 9-->
+               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
+               <param  type="data"  name="reffile9" label="Sample 9: Reference BAM file"/>  
+               <conditional name="genelist9">
+                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist9"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
+               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
+               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
+               <!-- END: 9 samples, yes refpairs, entry 9-->
+            </when> 
+         </conditional>
+      </when>                     
+      <when value="10">                     
+         <conditional name="usepair">
+            <param type="select" name="usepair1" label="Use reference alignment?" help="Using a reference bam file will allow the plots to display log2 fold changes instead of read count intensities.">
+               <option value="no">No</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="no">                     
+               <!-- START: 10 samples, no refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="hidden"  name="reffile1" value="na"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 1-->
+               <!-- START: 10 samples, no refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="hidden"  name="reffile2" value="na"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 2-->
+               <!-- START: 10 samples, no refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="hidden"  name="reffile3" value="na"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 3-->
+               <!-- START: 10 samples, no refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="hidden"  name="reffile4" value="na"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 4-->
+               <!-- START: 10 samples, no refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="hidden"  name="reffile5" value="na"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 5-->
+               <!-- START: 10 samples, no refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="hidden"  name="reffile6" value="na"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 6-->
+               <!-- START: 10 samples, no refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="hidden"  name="reffile7" value="na"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 7-->
+               <!-- START: 10 samples, no refpairs, entry 8-->
+               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
+               <param  type="hidden"  name="reffile8" value="na"/>  
+               <conditional name="genelist8">
+                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist8"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
+               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
+               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 8-->
+               <!-- START: 10 samples, no refpairs, entry 9-->
+               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
+               <param  type="hidden"  name="reffile9" value="na"/>  
+               <conditional name="genelist9">
+                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist9"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
+               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
+               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 9-->
+               <!-- START: 10 samples, no refpairs, entry 10-->
+               <param  type="data"  name="bamfile10" label="Sample 10: Input BAM file"/>
+               <param  type="hidden"  name="reffile10" value="na"/>  
+               <conditional name="genelist10">
+                  <param type="select" name="usegenelist10" label="Sample 10: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist10"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist10"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title10" value="plot10" label="Sample 10: Image title"/>  
+               <param  type="text"  name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>  
+               <param  type="text"  name="linecol10" value="tan3" label="Sample 10: Line plot color"/>  
+               <!-- END: 10 samples, no refpairs, entry 10-->
+            </when> 
+            <when value="yes">                     
+               <!-- START: 10 samples, yes refpairs, entry 1-->
+               <param  type="data"  name="bamfile1" label="Sample 1: Input BAM file"/>
+               <param  type="data"  name="reffile1" label="Sample 1: Reference BAM file"/>  
+               <conditional name="genelist1">
+                  <param type="select" name="usegenelist1" label="Sample 1: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist1"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist1"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title1" value="plot1" label="Sample 1: Image title"/>  
+               <param  type="text"  name="fraglen1" value="150" label="Sample 1: Expected fragment length"/>  
+               <param  type="text"  name="linecol1" value="green" label="Sample 1: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 1-->
+               <!-- START: 10 samples, yes refpairs, entry 2-->
+               <param  type="data"  name="bamfile2" label="Sample 2: Input BAM file"/>
+               <param  type="data"  name="reffile2" label="Sample 2: Reference BAM file"/>  
+               <conditional name="genelist2">
+                  <param type="select" name="usegenelist2" label="Sample 2: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist2"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist2"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title2" value="plot2" label="Sample 2: Image title"/>  
+               <param  type="text"  name="fraglen2" value="150" label="Sample 2: Expected fragment length"/>  
+               <param  type="text"  name="linecol2" value="blue" label="Sample 2: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 2-->
+               <!-- START: 10 samples, yes refpairs, entry 3-->
+               <param  type="data"  name="bamfile3" label="Sample 3: Input BAM file"/>
+               <param  type="data"  name="reffile3" label="Sample 3: Reference BAM file"/>  
+               <conditional name="genelist3">
+                  <param type="select" name="usegenelist3" label="Sample 3: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist3"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist3"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title3" value="plot3" label="Sample 3: Image title"/>  
+               <param  type="text"  name="fraglen3" value="150" label="Sample 3: Expected fragment length"/>  
+               <param  type="text"  name="linecol3" value="red" label="Sample 3: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 3-->
+               <!-- START: 10 samples, yes refpairs, entry 4-->
+               <param  type="data"  name="bamfile4" label="Sample 4: Input BAM file"/>
+               <param  type="data"  name="reffile4" label="Sample 4: Reference BAM file"/>  
+               <conditional name="genelist4">
+                  <param type="select" name="usegenelist4" label="Sample 4: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist4"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist4"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title4" value="plot4" label="Sample 4: Image title"/>  
+               <param  type="text"  name="fraglen4" value="150" label="Sample 4: Expected fragment length"/>  
+               <param  type="text"  name="linecol4" value="pink" label="Sample 4: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 4-->
+               <!-- START: 10 samples, yes refpairs, entry 5-->
+               <param  type="data"  name="bamfile5" label="Sample 5: Input BAM file"/>
+               <param  type="data"  name="reffile5" label="Sample 5: Reference BAM file"/>  
+               <conditional name="genelist5">
+                  <param type="select" name="usegenelist5" label="Sample 5: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist5"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist5"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title5" value="plot5" label="Sample 5: Image title"/>  
+               <param  type="text"  name="fraglen5" value="150" label="Sample 5: Expected fragment length"/>  
+               <param  type="text"  name="linecol5" value="slateblue" label="Sample 5: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 5-->
+               <!-- START: 10 samples, yes refpairs, entry 6-->
+               <param  type="data"  name="bamfile6" label="Sample 6: Input BAM file"/>
+               <param  type="data"  name="reffile6" label="Sample 6: Reference BAM file"/>  
+               <conditional name="genelist6">
+                  <param type="select" name="usegenelist6" label="Sample 6: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist6"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist6"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title6" value="plot6" label="Sample 6: Image title"/>  
+               <param  type="text"  name="fraglen6" value="150" label="Sample 6: Expected fragment length"/>  
+               <param  type="text"  name="linecol6" value="sienna" label="Sample 6: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 6-->
+               <!-- START: 10 samples, yes refpairs, entry 7-->
+               <param  type="data"  name="bamfile7" label="Sample 7: Input BAM file"/>
+               <param  type="data"  name="reffile7" label="Sample 7: Reference BAM file"/>  
+               <conditional name="genelist7">
+                  <param type="select" name="usegenelist7" label="Sample 7: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist7"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist7"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title7" value="plot7" label="Sample 7: Image title"/>  
+               <param  type="text"  name="fraglen7" value="150" label="Sample 7: Expected fragment length"/>  
+               <param  type="text"  name="linecol7" value="tomato" label="Sample 7: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 7-->
+               <!-- START: 10 samples, yes refpairs, entry 8-->
+               <param  type="data"  name="bamfile8" label="Sample 8: Input BAM file"/>
+               <param  type="data"  name="reffile8" label="Sample 8: Reference BAM file"/>  
+               <conditional name="genelist8">
+                  <param type="select" name="usegenelist8" label="Sample 8: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist8"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist8"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title8" value="plot8" label="Sample 8: Image title"/>  
+               <param  type="text"  name="fraglen8" value="150" label="Sample 8: Expected fragment length"/>  
+               <param  type="text"  name="linecol8" value="turquoise" label="Sample 8: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 8-->
+               <!-- START: 10 samples, yes refpairs, entry 9-->
+               <param  type="data"  name="bamfile9" label="Sample 9: Input BAM file"/>
+               <param  type="data"  name="reffile9" label="Sample 9: Reference BAM file"/>  
+               <conditional name="genelist9">
+                  <param type="select" name="usegenelist9" label="Sample 9: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist9"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist9"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title9" value="plot9" label="Sample 9: Image title"/>  
+               <param  type="text"  name="fraglen9" value="150" label="Sample 9: Expected fragment length"/>  
+               <param  type="text"  name="linecol9" value="violetred" label="Sample 9: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 9-->
+               <!-- START: 10 samples, yes refpairs, entry 10-->
+               <param  type="data"  name="bamfile10" label="Sample 10: Input BAM file"/>
+               <param  type="data"  name="reffile10" label="Sample 10: Reference BAM file"/>  
+               <conditional name="genelist10">
+                  <param type="select" name="usegenelist10" label="Sample 10: Gene list">
+                     <option value="no">Plot whole genome</option>
+                     <option value="yes">Provide restricted gene list</option>
+                  </param>
+                  <when value="no">                     
+                     <param type="hidden"  name="genelist10"  value="-1"/>
+                  </when>
+                  <when value="yes">
+                     <param type="data"  name="genelist10"  label="Choose the uploaded gene list for plotting"/>
+                  </when>
+               </conditional>
+               <param  type="text"  name="title10" value="plot10" label="Sample 10: Image title"/>  
+               <param  type="text"  name="fraglen10" value="150" label="Sample 10: Expected fragment length"/>  
+               <param  type="text"  name="linecol10" value="tan3" label="Sample 10: Line plot color"/>  
+               <!-- END: 10 samples, yes refpairs, entry 10-->
+            </when> 
+         </conditional>
+      </when>                     
+   </conditional>
+
+
+   
+   <param type="select" name="gene_database" label="Supported gene database: RefSeq, Ensembl">
+      <option value="ensembl">Ensembl</option>
+      <option value="refseq">RefSeq</option>
+   </param>
+   <param name="randomly_sample" size="10" type="text" value="1" label="Randomly sample the regions for plotting" help="This will randomly sample a portion of the whole genome or the gene lists. This option can be VERY useful if one just wants to get an overview in shorter time."/>
+   <conditional name="GO">
+      <param type="select" name="gene_order" label="Gene order algorithm">
+         <option value="total">Overall enrichment of the 1st profile</option>
+         <option value="hc">Hierarchical clustering</option>
+         <option value="max">Peak value of the 1st profile</option>
+         <option value="prod">Product of all profiles on the same region</option>
+         <option value="diff">Difference between the 1st and 2nd profiles</option>
+         <option value="km">K-means clustering</option>
+         <option value="none">No ranking algorithm applied. Use order in gene list.</option>
+      </param>
+      <when value="km">
+         <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
+         <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
+         <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+      </when>
+      <when value="total">
+         <param type="hidden" name="KNC" value="NA" />
+         <param type="hidden" name="MIT" value="NA" />
+         <param type="hidden" name="NRS" value="NA" />
+      </when>
+      <when value="hc">
+         <param type="hidden" name="KNC" value="NA" />
+         <param type="hidden" name="MIT" value="NA" />
+         <param type="hidden" name="NRS" value="NA" />
+      </when>
+      <when value="max">
+         <param type="hidden" name="KNC" value="NA" />
+         <param type="hidden" name="MIT" value="NA" />
+         <param type="hidden" name="NRS" value="NA" />
+      </when>
+      <when value="prod">
+         <param type="hidden" name="KNC" value="NA" />
+         <param type="hidden" name="MIT" value="NA" />
+         <param type="hidden" name="NRS" value="NA" />
+      </when>
+      <when value="diff">
+         <param type="hidden" name="KNC" value="NA" />
+         <param type="hidden" name="MIT" value="NA" />
+         <param type="hidden" name="NRS" value="NA" />
+      </when>
+      <when value="none">
+         <param type="hidden" name="KNC" value="NA" />
+         <param type="hidden" name="MIT" value="NA" />
+         <param type="hidden" name="NRS" value="NA" />
+      </when>
+   </conditional>
+   <param name="chunk_size" size="10" type="text" value="100" label="Chunk size for loading genes in batch" help="This parameter controls the behavior of coverage calculation. A smaller value implies lower memory footprint but may increase processing time."/>
+   <param name="quality_requirement" size="10" type="text" value="20" label="Mapping quality requirement" help="This is the Phred-scale mapping quality score. A score of 20 means an error rate of 1%."/>
+   <param type="select" name="standard_error" label="Plot standard errors" help="Standard errors will be rendered as shaded area around each curve.">
+      <option value="1">Yes</option>
+      <option value="0">No</option>
+   </param>
+
+   <param name="radius_size" size="10" type="text" value="0" label="Fraction of extreme values to be trimmed on both ends" help="The fraction of extreme values that will be trimmed on both ends. Eg. 0.05 will remove 5% of extreme values."/>
+   <param name="flooding_fraction" size="10" type="text" value="0.02" label="Heatmap flooding fraction" help="Default of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic."/>
+   <param type="select" name="smooth_method" label="Moving window width to smooth avg. profiles">
+      <option value="1">No</option>
+      <option value="3">Slightly</option>
+      <option value="5">Somewhat</option>
+      <option value="9">Quite</option>
+      <option value="13">Super</option>
+   </param>
+   <param name="shaded_area" size="10" type="text" value="0" label="Opacity of shaded area under curve" help="Suggested value between 0 and 0.5."/>
+<!--
+-->
+</inputs>
+
+<help>---TEST---</help>
+<outputs>
+   <data format="pdf" name="out_avg_png" />
+   <data format="pdf" name="out_hm_png" />
+   <data format="zip" name="out_zip"/>
+</outputs>
+</tool>
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/ngsplot_main/runNGSplot.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v1.0/ngsplot_main/runNGSplot.pl	Wed Mar 18 15:43:54 2015 -0400
@@ -0,0 +1,126 @@
+#!/usr/bin/perl -w
+use strict;
+use File::Basename 'dirname';
+use File::Spec;
+use Cwd 'abs_path';
+
+my @inputs = @ARGV;
+my @inputs2 = @inputs;
+
+my $genome_name = shift(@inputs);
+my $genomic_region_source_type__genomic_region = shift(@inputs);
+my $genomic_region_source_type__further_information = shift(@inputs);
+my $genomic_region_source_type__interval_size = shift(@inputs);
+my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_option = shift(@inputs);
+my $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size = shift(@inputs);
+my $numsamples = shift(@inputs);
+my $usepairs = shift(@inputs);
+
+#print STDERR "inputs @inputs\n";
+
+my $randfile = rand(100)."\.config\.txt";
+my $randfile2 = $randfile;
+$randfile2 =~ s/config\.txt/logfile/gm;
+
+my $outfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile");
+open(FILE,">$outfile");
+
+for (my $i=1;$i<=$numsamples;$i++) {
+   my $bamfile=shift(@inputs);
+   my $reffile=shift(@inputs);
+   my $usegenelist=shift(@inputs);
+   my $genelist=shift(@inputs);
+   my $title=shift(@inputs);
+   my $fraglen=shift(@inputs);
+   my $color=shift(@inputs);   
+   if ($usepairs eq 'yes') {
+      syswrite(FILE, "$bamfile\:$reffile\t$genelist\t$title\t$fraglen\t$color\n");
+   }else {
+      syswrite(FILE, "$bamfile\t$genelist\t$title\t$fraglen\t$color\n");
+   }
+}
+close(FILE);
+
+my $gene_database = shift(@inputs);
+my $randomly_sample = shift(@inputs);
+my $gene_order = shift(@inputs);
+my $knc = shift(@inputs);
+my $mit = shift(@inputs);
+my $nrs = shift(@inputs);
+my $chunk_size = shift(@inputs);
+my $quality_requirement = shift(@inputs);
+my $standard_error = shift(@inputs);
+my $radius_size = shift(@inputs);
+my $flooding_fraction = shift(@inputs);
+my $smooth_method = shift(@inputs);
+my $shaded_area = shift(@inputs);
+my $out_name = shift(@inputs);
+my $out_avg_name = shift(@inputs);
+my $out_hm_name = shift(@inputs);
+
+
+my $G = $genome_name;
+my $R = $genomic_region_source_type__genomic_region;
+my $C = $outfile;
+my $O = $out_name;
+my $O2 = $out_avg_name;
+my $O3 = $out_hm_name;
+my $F = $genomic_region_source_type__further_information;
+my $D = $gene_database;
+my $L = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
+my $N = $genomic_region_source_type__flanking_region_option_source_type__flanking_region_size;
+my $RB = $radius_size;
+my $S = $randomly_sample;
+my $CS = $chunk_size;
+my $MQ = $quality_requirement;
+my $IN = $genomic_region_source_type__interval_size;
+my $SE = $standard_error;
+my $MW = $smooth_method;
+my $H = $shaded_area;
+my $GO = $gene_order;
+my $KNC = $knc;
+my $MIT = $mit;
+my $NRS = $nrs;
+my $FC = $flooding_fraction;
+
+if ($GO eq 'km') {
+   $GO = "$GO -KNC $KNC -MIT $MIT -NRS $NRS";
+}
+
+my $logfile = File::Spec->catfile(abs_path(dirname(__FILE__)),"$randfile2");
+open(FILE2,">>$logfile");
+my $cmd5="pwd >> $logfile 2>&1";
+system($cmd5);
+
+my $cmd='';
+if (($R eq 'tss')||($R eq 'tes')) {
+   $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
+}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_region_size') {
+   if ($IN eq 'automatic') {
+      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H >> $logfile 2>&1";
+   }else {
+      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -L $L -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN  >> $logfile 2>&1";
+   }
+}elsif ($genomic_region_source_type__flanking_region_option_source_type__flanking_region_option eq 'flanking_floating_size') {
+   if ($IN eq 'automatic') {
+      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H  >> $logfile 2>&1";
+   }else {
+      $cmd = "ngs.plot.r -Galaxy 1 -P 0 -G $G -R $R -C $C -O $O -O2 $O2 -O3 $O3 -D $D -N $N -S $S -GO $GO -CS $CS -MQ $MQ -SE $SE -RB $RB -FC $FC -MW $MW -H $H -IN $IN  >> $logfile 2>&1";
+   }
+}
+my $cmd2="cp data.zip $O";
+my $cmd3="rm $outfile";
+my $cmd4="rm $logfile";
+syswrite(FILE2, "\n$cmd\n");
+syswrite(FILE2, "\n$cmd2\n");
+syswrite(FILE2, "\n$cmd3\n");
+syswrite(FILE2, "\n$cmd4\n\n");
+
+system($cmd);
+system($cmd2);
+system($cmd3);
+system($cmd4);
+
+close(FILE2);
+
+
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/ngsplot_replot/replot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v1.0/ngsplot_replot/replot.xml	Wed Mar 18 15:43:54 2015 -0400
@@ -0,0 +1,157 @@
+<tool id="replot" name="replot">
+<command interpreter="perl">
+#if $outtype.outtype2 == "prof":
+   runreplot.pl $input_zipfile $outtype.outtype2 $output_filename 
+   $outtype.WD
+   $outtype.HG
+   $outtype.SE
+   $outtype.H
+   $outtype.MW
+   $outtype.Y.Y2
+   $outtype.Y.Y3
+   $outtype.LEG
+   $outtype.BOX
+   $outtype.VLN
+   $outtype.XYL
+   $outtype.LWD
+   $outtype.FS
+#else if $outtype.outtype2 == "heatmap":
+   runreplot.pl $input_zipfile $outtype.outtype2 $output_filename 
+   $outtype.GO.GO2
+   $outtype.GO.KNC
+   $outtype.GO.MIT
+   $outtype.GO.NRS
+   $outtype.LOW
+   $outtype.RR
+   $outtype.FC
+   $outtype.CO
+   $outtype.CD
+   $outtype.FS
+   dummy
+   dummy
+   dummy
+#end if:
+
+</command>
+
+<!-->
+
+
+<-->
+
+<inputs>
+   <param  type="data"  name="input_zipfile" multiple="false" label="Input zip file created by ngsplot"/>
+
+   <conditional name="outtype">
+      <param  type="select"  name="outtype2" label="Select figure type to replot">
+         <option value="prof">Coverage Profile</option>
+         <option value="heatmap">Heatmap</option>
+      </param>
+
+      <when value="prof">
+         <param type="text" name="WD" value="8" label="Image width in inches" />
+         <param type="text" name="HG" value="7" label="Image height in inches" />
+         <param type="select" name="SE" label="Standard error shading" >
+            <option value="1">Yes, include standard error shading</option>
+            <option value="0">No, exclude standard error shading</option>
+         </param>
+         <param type="text" name="H" value="0" label="Opacity of shaded area under each curve" help="Use 0 for no shading. Suggested value of between 0 and 0.5 will add a semi-transparent shade under each curve."/>
+         <param type="text" name="MW" value="1" label="Moving window width to smooth average profiles" help="The unit of the window size is a data point. In ngs.plot, the number of data points on the X-axis is 100. A moving window width of 10 means averaging over 10% of the entire X-axis."/>
+         <conditional name="Y">
+            <param type="select" name="Y2" label="Define Y-axis scale?" >
+               <option value="no">No, let program decide</option>
+               <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+               <param type="text" name="Y3" value="0,100" label="Y-axis min_val,max_val" help="Enter minimum and maximum value separated by comma" />
+            </when>
+            <when value="no">
+               <param type="hidden" name="Y3" value="na" label="test"/>
+            </when>
+         </conditional>
+         <param type="select" name="LEG" label="Draw legend?" >
+            <option value="1">Yes</option>
+            <option value="0">No</option>
+         </param>
+         <param type="select" name="BOX" label="Draw box around plot?" >
+            <option value="1">Yes</option>
+            <option value="0">No</option>
+         </param>
+         <param type="select" name="VLN" label="Draw vertical lines?" >
+            <option value="1">Yes</option>
+            <option value="0">No</option>
+         </param>
+         <param type="select" name="XYL" label="Draw axis labels?" >
+            <option value="1">Yes</option>
+            <option value="0">No</option>
+         </param>
+         <param type="text" name="LWD" value="3" label="Line width" />
+         <param type="text" name="FS" value="12" label="Font size" />
+<!-->
+<-->
+
+      </when>
+      <when value="heatmap">
+         <conditional name="GO">
+            <param type="select" name="GO2" label="Gene order algorithm" >
+               <option value="total">Overall enrichment of the 1st profile (default)</option>
+               <option value="hc">Hierarchial clustering</option>
+               <option value="max">Peak value of the 1st profile</option>
+               <option value="prod">Product of all profiles on the same region</option>
+               <option value="diff">Difference between 1st and 2nd profiles</option>
+               <option value="km">K-means clustering.</option>
+               <option value="none">No ranking algorithm applied, use order in gene list.</option>
+            </param>
+            <when value="km">
+               <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
+               <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
+               <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+            <when value="total">
+               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
+               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
+               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+            <when value="hc">
+               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
+               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
+               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+            <when value="max">
+               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
+               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
+               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+            <when value="prod">
+               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
+               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
+               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+            <when value="diff">
+               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
+               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
+               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+            <when value="none">
+               <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
+               <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
+               <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
+            </when> 
+         </conditional>
+         <param type="text" name="LOW" value="10" label="Low count cutoff in rank-based normalization" help="This number is in raw read counts."/>
+         <param type="text" name="RR" value="30" label="Reduce ratio" help="This controls the heatmap height. The smaller the value, the taller the heatmap." />
+         <param type="text" name="FC" value="0.02" label="Flooding fraction" help="The default value of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic." />
+         <param type="text" name="CO" value="default" label="Color for heatmap" help="For non bam-pair plots, input a single color. For bam-pair plots, use color-tri format (neg_color:[neu_color]:pos_color). Hint: must use R colors, such as darkgreen, yellow and blue2. The neutral color is optional(default=black)." />
+         <param type="text" name="CD" value="0.6" label="Color distribution for heatmap" help="Must be a positive number. Hint: lower values give more widely spaced colors at the negative end. In other words, they shift the neutral color to positive values. If set to 1, the neutral color represents 0(i.e. no bias). If set to >1, the neutral color represents a negative value." />
+         <param type="text" name="FS" value="12" label="Font size" />
+      </when>
+   </conditional>
+<!--
+-->
+</inputs>
+
+<help>---TEST---</help>
+<outputs>
+   <data format="pdf" name="output_filename" />
+</outputs>
+</tool>
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/ngsplot_replot/runreplot.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v1.0/ngsplot_replot/runreplot.pl	Wed Mar 18 15:43:54 2015 -0400
@@ -0,0 +1,63 @@
+#!/usr/bin/perl -w
+use strict;
+use File::Basename 'dirname';
+use File::Spec;
+use Cwd 'abs_path';
+
+my $input_file = $ARGV[0];
+my $output_type = $ARGV[1];
+my $output_filename = $ARGV[2];
+
+my $cmd1 = "cp $input_file data.zip";
+my $cmd2 = "";
+my $cmd3 = "mv output.pdf $output_filename";
+
+my $FS = "";
+if ($output_type eq 'prof') {
+   my $WD = "-WD $ARGV[3]";
+   my $HG = "-HG $ARGV[4]";
+   my $SE = "-SE $ARGV[5]";
+   my $H = "-H $ARGV[6]";
+   my $MW = "-MW $ARGV[7]";
+   my $Y = "-Y $ARGV[8]";
+   my $YAS = "-YAS $ARGV[9]";
+   my $LEG = "-LEG $ARGV[10]";
+   my $BOX = "-BOX $ARGV[11]";
+   my $VLN = "-VLN $ARGV[12]";
+   my $XYL = "-XYL $ARGV[13]";
+   my $LWD = "-LWD $ARGV[14]";
+   $FS = "-FS $ARGV[15]";
+
+   if ($Y =~ /no$/gm) {
+      $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS";
+   }else {
+      $cmd2 = "replot.r $output_type -I data.zip -O output $WD $HG $SE $H $MW $LEG $BOX $VLN $XYL $LWD $FS $YAS";
+   }
+}elsif ($output_type eq 'heatmap') {
+   my $GO = "-GO $ARGV[3]";
+   my $KNC = "-KNC $ARGV[4]";
+   my $MIT = "-MIT $ARGV[5]";
+   my $NRS = "-NRS $ARGV[6]";
+   my $LOW = "-LOW $ARGV[7]";
+   my $RR = "-RR $ARGV[8]";
+   my $FC = "-FC $ARGV[9]";
+   my $CO = "-CO $ARGV[10]";
+   my $CD = "-CD $ARGV[11]";
+   $FS = "-FS $ARGV[12]";
+   my $DUM1 = $ARGV[13];
+   my $DUM2 = $ARGV[14];
+   my $DUM3 = $ARGV[15];
+
+   if ($CO =~ /default/gm) { $CO = ""; }
+
+   if ($GO =~ /km$/gm) {
+      $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO $KNC $MIT $NRS"; 
+   }else {
+      $cmd2 = "replot.r $output_type -I data.zip -O output $LOW $RR $FC $CO $CD $FS $GO";
+   }
+}
+system($cmd1);
+system($cmd2);
+system($cmd3);
+
+
diff -r 795270a5555c -r b2d5006b82b8 ngsplot_galaxytoolshed_v1.0/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed_v1.0/tool_dependencies.xml	Wed Mar 18 15:43:54 2015 -0400
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ngsplot" version="2.47.1">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">tar -xzvf ngsplot-2.47.1.tar.gz</action>
+                <action type="move_directory_files">
+                    <source_directory>ngsplot</source_directory>
+                    <destination_directory>$INSTALL_DIR/ngsplot</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ngsplot/bin</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="NGSPLOT" action="prepend_to">$INSTALL_DIR/ngsplot</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            This installation of ngsplot assumes that R v3.0+ has already been installed on your system, including R packages doMC and caTools, as well as bioconductor packages BSgenome, Rsamtools, and ShortRead. For more information on how to install these additional R packages, see https://code.google.com/p/ngsplot/.
+        </readme>
+    </package>
+</tool_dependency>