# HG changeset patch
# User ngsplot
# Date 1426702090 14400
# Node ID e6028c2c3da38fd5fcb26b1430c45824648524a3
Uploaded
diff -r 000000000000 -r e6028c2c3da3 ngsplot_galaxytoolshed/ngsplot_intro/intro.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed/ngsplot_intro/intro.xml Wed Mar 18 14:08:10 2015 -0400
@@ -0,0 +1,67 @@
+
+
+
+
+
+#if $numsamples.numsamples2 == "1":
+ runNGSplot.pl
+ $genome_name
+
+#else if $numsamples.numsamples2 == "5":
+ runNGSplot.pl
+ $genome_name
+
+#end if:
+
+
+
+
+
+**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.
+
+
+
+
+
+
diff -r 000000000000 -r e6028c2c3da3 ngsplot_galaxytoolshed/ngsplot_main/ngsplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed/ngsplot_main/ngsplot.xml Wed Mar 18 14:08:10 2015 -0400
@@ -0,0 +1,3174 @@
+
+
+#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:
+
+
+
+
+<-->
+
+
+
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+
+
+
+
+---TEST---
+
+
+
+
+
+
diff -r 000000000000 -r e6028c2c3da3 ngsplot_galaxytoolshed/ngsplot_main/runNGSplot.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed/ngsplot_main/runNGSplot.pl Wed Mar 18 14:08:10 2015 -0400
@@ -0,0 +1,144 @@
+#!/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");
+
+#my $outfile2=$outfile;
+#my $logfile2=$logfile;
+#$outfile2 =~ s/^\S+\///gm;
+#$logfile2 =~ s/^\S+\///gm;
+#my $cmd3="cp $outfile /home/galaxy/Programs/galaxy-dist/tools/ngsplot/a$outfile2";
+#my $cmd4="cp $logfile /home/galaxy/Programs/galaxy-dist/tools/ngsplot/a$logfile2";
+
+
+system($cmd);
+system($cmd2);
+system($cmd3);
+system($cmd4);
+
+close(FILE2);
+
+#my $count=0;
+#foreach my $entry (@inputs2) {
+# $count++;
+# syswrite(FILE2, "$count: $entry\n");
+#}
+
+
+
+
+
+
diff -r 000000000000 -r e6028c2c3da3 ngsplot_galaxytoolshed/ngsplot_replot/replot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed/ngsplot_replot/replot.xml Wed Mar 18 14:08:10 2015 -0400
@@ -0,0 +1,157 @@
+
+
+#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:
+
+
+
+
+
+
+<-->
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<-->
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+---TEST---
+
+
+
+
diff -r 000000000000 -r e6028c2c3da3 ngsplot_galaxytoolshed/ngsplot_replot/runreplot.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ngsplot_galaxytoolshed/ngsplot_replot/runreplot.pl Wed Mar 18 14:08:10 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);
+
+