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changeset 18:565118df598a draft

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Uploaded 20170531
author fabio
date Wed, 31 May 2017 11:07:22 -0400
parents 81faa1567178
children 09b34f32dc7d
files ._ETn_example ._example ._loadandplot.R ._plotwithscale.R ._testandplot.R ETn_example/._.DS_Store ETn_example/._Control.bed ETn_example/._DESCRIPTION.txt ETn_example/._ETn_fixed.bed ETn_example/._Recombination_hotspots.txt ETn_example/._features.header ETn_example/._regions.header ETn_example/Control.bed ETn_example/DESCRIPTION.txt ETn_example/ETn_fixed.bed ETn_example/Recombination_hotspots.txt ETn_example/features.header ETn_example/regions.header example/._.DS_Store example/._Controls_regions.bed example/._DESCRIPTION.txt example/._Elements1_regions.bed example/._Elements2_regions.bed example/._Elements3_regions.bed example/._Feature1.bed example/._Feature2.bed example/._features.header.bed.txt example/._regions.header.txt example/Controls_regions.bed example/DESCRIPTION.txt example/Elements1_regions.bed example/Elements2_regions.bed example/Elements3_regions.bed example/Feature1.bed example/Feature2.bed example/features.header.bed.txt example/regions.header.txt iwtomics/ETn_example/._.DS_Store iwtomics/ETn_example/._Control.bed iwtomics/ETn_example/._DESCRIPTION.txt iwtomics/ETn_example/._ETn_fixed.bed iwtomics/ETn_example/._Recombination_hotspots.txt iwtomics/ETn_example/._features.header iwtomics/ETn_example/._regions.header iwtomics/ETn_example/Control.bed iwtomics/ETn_example/DESCRIPTION.txt iwtomics/ETn_example/ETn_fixed.bed iwtomics/ETn_example/Recombination_hotspots.txt iwtomics/ETn_example/features.header iwtomics/ETn_example/regions.header iwtomics/example/._.DS_Store iwtomics/example/._Controls_regions.bed iwtomics/example/._DESCRIPTION.txt iwtomics/example/._Elements1_regions.bed iwtomics/example/._Elements2_regions.bed iwtomics/example/._Elements3_regions.bed iwtomics/example/._Feature1.bed iwtomics/example/._Feature2.bed iwtomics/example/._features.header.bed.txt iwtomics/example/._regions.header.txt iwtomics/example/Controls_regions.bed iwtomics/example/DESCRIPTION.txt iwtomics/example/Elements1_regions.bed iwtomics/example/Elements2_regions.bed iwtomics/example/Elements3_regions.bed iwtomics/example/Feature1.bed iwtomics/example/Feature2.bed iwtomics/example/features.header.bed.txt iwtomics/example/regions.header.txt loadandplot.R loadandplot.xml macros.xml plotwithscale.R plotwithscale.xml testandplot.R testandplot.xml
diffstat 76 files changed, 16952 insertions(+), 15816 deletions(-) [+]
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Binary file ._ETn_example has changed
Binary file ._example has changed
Binary file ._loadandplot.R has changed
Binary file ._plotwithscale.R has changed
Binary file ._testandplot.R has changed
Binary file ETn_example/._.DS_Store has changed
Binary file ETn_example/._Control.bed has changed
Binary file ETn_example/._DESCRIPTION.txt has changed
Binary file ETn_example/._ETn_fixed.bed has changed
Binary file ETn_example/._Recombination_hotspots.txt has changed
Binary file ETn_example/._features.header has changed
Binary file ETn_example/._regions.header has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/Control.bed	Wed May 31 11:07:22 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/DESCRIPTION.txt	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,21 @@
+This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
+In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
+fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
+of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
+used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
+sites).
+Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
+particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
+hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
+fraction of the 1-kb window that is covered by recombination hotspots
+
+Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
+Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
+endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
+12(6): 1-41.
+Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
+Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
+active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
+Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
+B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
+genome. Genetics. 191: 757-764.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/ETn_fixed.bed	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,1296 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/Recombination_hotspots.txt	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2438 @@
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+chr9	118910538	118974538	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.491	1	1	1	1	1	1	1	1	0.509	0	0	0	0	0	0	0	0	0	0
+chr9	121627136	121691136	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/features.header	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,1 @@
+Recombination_hotspots.txt	Recomb_hot	Recombination hotspots
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/regions.header	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2 @@
+Control.bed	Control	Control
+ETn_fixed.bed	ETn_fixed	ETn fixed
\ No newline at end of file
Binary file example/._.DS_Store has changed
Binary file example/._Controls_regions.bed has changed
Binary file example/._DESCRIPTION.txt has changed
Binary file example/._Elements1_regions.bed has changed
Binary file example/._Elements2_regions.bed has changed
Binary file example/._Elements3_regions.bed has changed
Binary file example/._Feature1.bed has changed
Binary file example/._Feature2.bed has changed
Binary file example/._features.header.bed.txt has changed
Binary file example/._regions.header.txt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Controls_regions.bed	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,35 @@
+chr1	91399892	91499892
+chr1	116447079	116547079
+chr2	231381109	231481109
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+chr3	134345017	134445017
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+chr12	15210277	15310277
+chr13	91106037	91206037
+chr13	91518822	91618822
+chr13	98959030	99059030
+chr15	39087176	39187176
+chr17	58542142	58642142
+chr18	12199823	12299823
+chr20	8173704	8273704
+chr21	16255112	16355112
+chr21	45089115	45189115
+chrX	23898983	23998983
+chrX	37029585	37129585
+chrX	103593349	103693349
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/DESCRIPTION.txt	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2 @@
+This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", 
+corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements1_regions.bed	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,25 @@
+chr2	49960150	50060150
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+chr14	100464166	100564166
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements2_regions.bed	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,20 @@
+chr1	65942901	66042901
+chr1	117128102	117228102
+chr1	190338169	190438169
+chr2	227365478	227465478
+chr6	50856764	50956764
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+chr7	38228726	38328726
+chr7	51115898	51215898
+chr7	150325760	150425760
+chr8	25475691	25575691
+chr9	73374609	73474609
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+chr12	48151882	48251882
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+chr15	31430278	31530278
+chr15	65610815	65710815
+chr17	40766223	40866223
+chr20	17245048	17345048
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements3_regions.bed	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,28 @@
+chr1	49721616	49821616
+chr1	95059425	95159425
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+chr2	73790843	73890843
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+chr6	147019529	147119529
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+chr16	66789863	66889863
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+chr21	15966609	16066609
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Feature1.bed	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,5400 @@
+chr1	91399892	91401892	0.914729028492568
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+++ b/example/Feature2.bed	Wed May 31 11:07:22 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/features.header.bed.txt	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2 @@
+Feature1.bed	ftr1	Feature 1
+Feature2.bed	ftr2	Feature 2
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/regions.header.txt	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,4 @@
+Elements1_regions.bed	elem1	Elements 1
+Elements2_regions.bed	elem2	Elements 2
+Elements3_regions.bed	elem3	Elements 3
+Controls_regions.bed	control	Controls
\ No newline at end of file
Binary file iwtomics/ETn_example/._.DS_Store has changed
Binary file iwtomics/ETn_example/._Control.bed has changed
Binary file iwtomics/ETn_example/._DESCRIPTION.txt has changed
Binary file iwtomics/ETn_example/._ETn_fixed.bed has changed
Binary file iwtomics/ETn_example/._Recombination_hotspots.txt has changed
Binary file iwtomics/ETn_example/._features.header has changed
Binary file iwtomics/ETn_example/._regions.header has changed
--- a/iwtomics/ETn_example/Control.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/iwtomics/ETn_example/DESCRIPTION.txt	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
-In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
-fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
-of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
-used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
-sites).
-Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
-particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
-hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
-fraction of the 1-kb window that is covered by recombination hotspots
-
-Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
-Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
-endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
-12(6): 1-41.
-Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
-Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
-active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
-Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
-B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
-genome. Genetics. 191: 757-764.
\ No newline at end of file
--- a/iwtomics/ETn_example/ETn_fixed.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1296 +0,0 @@
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--- a/iwtomics/ETn_example/Recombination_hotspots.txt	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2438 +0,0 @@
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-chr15	101761129	101825189	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.519	1	1	1	1	0.421	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr15	102277311	102341647	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.061	1	1	1	1	1	1	1	1	0.603	0	0	0	0	0	0	0	0	0	0	0	0	0.397	1	1	1	1	1	1	1	1	1	1	0.603	0	0	0	0	0	0	0
-chr16	7653172	7717511	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.453	0	0.547	1	1	1	1	1	1	1
-chr16	8070319	8134641	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	9164091	9228433	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr16	11159555	11223876	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr16	16032818	16097157	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	16914958	16979293	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr16	19520197	19591683	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	19779271	19843612	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	22293249	22357587	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr16	27131666	27195726	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	27242523	27306862	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	27649432	27713777	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	28636231	28700568	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	29524264	29588325	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	29645377	29709711	1	0.992	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	29895348	29959675	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	30432362	30496423	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.296	1	0.704	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	30874010	30945486	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	30971791	31036131	1	1	0.928	0	0	0	0	0	0.072	1	1	0.928	0	0	0	0	0	0	0	0	0	0	0.072	1	1	1	1	1	0.928	0	0	0	0	0	0	0	0	0	0	0	0	0.412	1	1	1	0.588	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	31356015	31420351	1	1	0.016	0	0	0	0	0	0	0	0	0	0	0	0	0	0.984	1	1	0.016	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	31544155	31608215	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.88	1	1	1	1	1	1	1	1	1	1	1	0.12	0	0	0	0	0
-chr16	31918232	31982292	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.043	1	0.957	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.103	1	1	0.897	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	34625490	34689817	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	36202740	36267079	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.595	1	1	1	1	0.405	0	0	0	0	0	0.595	1	1	0.405	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	36325256	36389591	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	37096473	37160798	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	38302930	38366991	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	38799139	38868667	0	0	0	0	0.668	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.332	0	0	0.668	1	1	1	1	1	0.804	0.196	1	1	1	1	1	1	1	1	1	1	0.804	0	0	0	0	0	0	0.196	1	1	1	1	1	0.804	0.196	1	1	1
-chr16	39029485	39093806	1	1	1	0.471	0	0	0	0	0.529	1	1	1	0.471	0	0.529	1	1	1	1	1	1	1	1	1	1	0.471	0	0	0	0.529	1	1	1	1	1	1	0.15	0	0	0	0	0.85	1	1	1	1	0.15	0	0	0.85	1	1	1	1	1	1	1	1	1	0.15	0	0	0.85	1
-chr16	40954161	41018479	0	0	0	0	0	0.826	1	1	0.174	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	44551564	44624431	0	0	0	0	0	0.904	1	1	0.096	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.904	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.229	0	0	0.771	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr16	46964652	47028712	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.377	1	0.623	0	0	0
-chr16	50131192	50195528	0	0	0	0	0	0	0	0	0	0	0	0.807	1	1	0.193	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	51481294	51545617	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.959	1	1	1	1	1	1	1	1	1	0.718	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	54102982	54167315	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr16	54998681	55063001	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	136924763	136988763	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.027	1	1	1	0.973	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.027	1	1	1	1	1	1	0.973	0	0	0	0	0	0	0	0	0	0	0	0	0.027	1	1	1	1	1	1	1	1
-chr1	136988763	137052763	0.973	0	0	0	0	0.027	1	1	1	1	1	0.973	0	0	0	0	0	0	0	0	0	0.027	1	1	1	1	1	1	0.973	0	0	0	0	0	0.027	1	1	1	1	1	1	1	0.973	0.027	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr1	137229123	137293123	1	1	1	1	1	1	1	1	1	1	1	0.613	0	0	0	0	0	0	0.387	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.613	0	0	0	0	0	0	0	0	0	0	0.387	1	1	1	1	1	1	1	1	0.613	0	0	0	0.387	1	1	1	0.613	0.387	1
-chr1	137689172	137753172	0.458	1	1	1	1	1	1	1	1	1	1	1	1	1	0.542	0	0	0.458	1	1	0.542	0.458	1	1	1	1	1	0.542	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	138803292	138867292	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	139995038	140059038	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	159052908	159116908	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.194	1	1	1	1	1	1	1	0.806	0	0.194	1	1	1	1	1	1	1	1	1	1	0.806	0	0	0	0	0	0.194	1	1	1
-chr1	162345948	162409948	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.234	1	0.766	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	163888959	163952959	1	1	1	1	1	1	1	1	1	1	1	1	1	0.755	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.245	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.755	0	0	0	0	0
-chr1	164146377	164210377	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.317	1	1	0.683	0	0
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-chr1	170078935	170142935	0	0	0	0	0	0	0	0	0.875	1	1	0.125	0	0	0	0	0	0	0	0	0	0	0.875	1	1	1	1	1	0.125	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.875	1	1	1	1	0.125	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	170185390	170249390	0	0	0	0	0	0	0	0	0	0	0.33	1	1	1	1	1	1	1	1	1	0.67	0	0	0	0.33	1	1	0.67	0	0	0	0.33	1	1	1	1	1	1	1	0.67	0	0.33	1	1	1	1	1	0.67	0	0	0	0	0	0	0	0	0.33	1	1	1	1	1	1	0.67
-chr1	170249390	170313390	0	0	0	0	0	0	0	0	0.33	1	1	1	1	0.67	0	0	0	0	0	0	0	0	0.33	1	1	1	1	1	1	1	1	1	0.67	0	0	0	0.33	1	1	0.67	0	0	0	0	0	0	0	0.33	1	1	1	1	0.67	0	0	0	0.33	1	1	0.67	0	0.33	1	1
-chr1	173284896	173348896	1	1	1	0.164	0	0	0	0.836	1	1	0.164	0	0	0.836	1	1	1	1	1	1	0.164	0	0	0	0	0	0	0.836	1	1	1	1	1	1	1	0.164	0.836	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.164	0	0	0	0	0	0	0	0	0	0	0.836
-chr1	174231860	174295860	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.2	0	0	0.8	1	1	1	1	1	1	1
-chr1	175209865	175273865	1	1	1	1	1	1	1	1	1	0.195	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.805	1	1	1	1	1	1	1	1	1	0.195	0	0	0.805	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr1	176812441	176876441	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.619	0	0	0	0	0	0.381	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.619	0	0	0	0
-chr1	179114819	179178819	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	183090720	183154720	0	0	0	0	0	0	0	0	0	0	0	0.66	1	1	0.34	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.66	1	1	0.34	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	188499484	188563484	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr1	189902115	189966115	0	0.055	1	1	1	1	0.945	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	190477513	190541513	1	1	0.547	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.453	1	1	0.547	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	191934479	191998479	0.792	0	0.208	1	1	1	1	0.792	0.208	1	1	1	1	1	1	1	1	1	0.792	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.208	1	1	1	1	1	1	0.792	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr1	196512385	196576385	0	0	0	0	0	0.114	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.886	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr10	12363669	12427669	0	0	0	0	0	0	0.966	1	1	1	0.034	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr10	13778671	13842671	0	0	0	0	0	0	0	0	0	0	0.968	1	1	1	1	0.032	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.968	1	1	1	1	1	1	1	0.032	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr10	14108714	14172714	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.989	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.011	1	1	1	1	1	1	0.989	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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-chr9	44257286	44321286	1	1	0.902	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.098	1	1	0.902	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	44893563	44957563	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.375	1	1	1	1	1	1	1	1	0.625	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	45496156	45560156	1	1	0.032	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	45700064	45764064	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	47438414	47502414	1	1	1	1	1	1	1	1	1	1	1	1	0.774	0	0	0	0	0	0	0.226	1	1	1	1	1	1	1	0.774	0	0	0	0.226	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr9	47502414	47566414	1	1	1	1	1	1	1	1	1	1	1	0.774	0.226	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.774	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.226	1	1	1	0.774	0	0	0	0	0	0	0	0.226	1	1	1
-chr9	47566414	47630414	1	1	1	1	1	1	1	1	1	1	0.774	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.226	1	1	1	1	1	0.774	0.226	1	0.774	0.226	1	1	1	1	1	1
-chr9	47630414	47694414	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.774	0	0	0	0	0	0.226	1	1	1	1	1	1	0.774	0	0	0	0	0.226	1	1	1	1	1	1	1	1	0.774	0	0.226	1	1	1	1	1	1	1	0.774	0.226	1	1	1	1
-chr9	48557242	48621242	1	1	1	1	1	1	1	0.946	0	0.054	1	0.946	0.054	1	1	1	1	0.946	0	0	0	0	0	0.054	1	1	0.946	0	0	0	0	0	0	0.054	1	0.946	0	0	0	0	0	0	0	0	0	0.054	1	1	1	1	1	1	1	1	1	1	1	1	1	0.946	0	0.054	1	1
-chr9	56295240	56359240	1	1	1	1	1	1	1	1	1	0.948	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.052	1	1	1	1	1	1
-chr9	56707178	56771178	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.99	1	1	1	1	1	0.01	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	57431374	57495374	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.186	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.814	0	0	0	0	0	0	0	0	0	0	0	0.186	1	1	1	1	1	1	1	1	1
-chr9	59569429	59633429	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	62718979	62782979	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	63147522	63211522	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	63788832	63852832	1	1	0.45	0	0	0	0	0	0	0	0	0	0	0	0.55	1	1	1	1	0.45	0	0	0	0	0	0	0.55	1	1	1	1	1	1	1	1	1	0.45	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	69050403	69114403	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.121	1	1	1	1	1	1	1	1	0.879	0	0.121	1	1	0.879	0	0	0	0.121	1	1	1	1	1	1	1	0.879	0	0	0
-chr9	69176049	69240049	1	1	1	1	0.233	0	0	0	0	0	0	0.767	1	1	0.233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.767	1	1	0.233	0	0	0	0	0.767	1	1	1	1	0.233	0	0	0	0
-chr9	69240049	69304049	0	0	0	0	0	0.767	1	1	1	1	0.233	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.767	1	0.233	0	0	0	0	0	0	0	0	0	0	0
-chr9	71796844	71860844	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.562	1	1	0.438	0	0	0	0	0	0	0	0	0	0	0.562	1	1	1
-chr9	74791622	74855622	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.34	1	1	0.66	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	79491629	79555629	0	0	0	0	0	0.347	1	1	1	1	1	0.653	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.347	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr9	79932960	79996960	0.322	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.678	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.322	0	0	0	0	0	0	0.678	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-chr9	84626957	84690957	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.675	1	1	0.325	0	0	0	0
-chr9	96193779	96257779	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.949	1	1	0.051	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.949	1	1	0.051	0	0	0	0	0
-chr9	107312141	107376141	1	1	0.689	0.311	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.689	0	0	0	0	0	0	0.311	1	1	1	1	0.689	0	0	0	0.311	1	1	1	1	1	1	1	1	1	1	1
-chr9	107376141	107440141	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.689	0	0	0	0	0	0	0	0	0.311	1	1	0.689	0	0	0	0	0	0	0	0	0	0	0.311	1	1	1	1	1	1	1	1
-chr9	107462650	107526650	0	0	0	0	0	0	0	0	0	0	0.82	1	1	1	1	0.18	0	0	0	0	0	0	0	0.82	1	1	1	1	1	0.18	0.82	1	0.18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.82	1	1	0.18	0	0.82	1	1	0.18
-chr9	107526650	107590650	0	0	0.82	1	1	1	1	1	1	0.18	0	0.82	1	1	1	1	1	1	0.18	0	0.82	1	1	1	1	0.18	0	0	0	0.82	1	1	0.18	0	0.82	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	0.18	0	0.82	1	0.18	0	0	0	0	0	0.82	1	1
-chr9	107590650	107654650	0.18	0.82	1	1	1	1	1	1	1	1	1	1	0.18	0	0	0	0	0	0	0	0	0	0	0	0	0.82	1	1	1	1	1	1	1	1	1	1	0.18	0	0	0	0	0	0.82	1	1	1	0.18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.82
-chr9	107848560	107912560	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.73	1	0.27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	107941738	108005738	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.908	1	0.092	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	108683437	108747437	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	108962296	109026296	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.466	1	1	1	0.534	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	109947901	110011901	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	110485254	110549254	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	110616374	110680374	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.544	1	1	1	1	1	1	1	1	1	0.456	0.544	1	1	1	1	1	1	0.456	0.544	1	1	0.456	0.544	1	1	1
-chr9	111968818	112032818	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-chr9	113836504	113900504	0	0	0.457	1	1	1	1	0.543	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.457	1	1	1	1	1	1	1	1	0.543	0	0	0	0	0.457	1	1	1	1
-chr9	118910538	118974538	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.491	1	1	1	1	1	1	1	1	0.509	0	0	0	0	0	0	0	0	0	0
-chr9	121627136	121691136	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- a/iwtomics/ETn_example/features.header	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Recombination_hotspots.txt	Recomb_hot	Recombination hotspots
\ No newline at end of file
--- a/iwtomics/ETn_example/regions.header	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Control.bed	Control	Control
-ETn_fixed.bed	ETn_fixed	ETn fixed
\ No newline at end of file
Binary file iwtomics/example/._.DS_Store has changed
Binary file iwtomics/example/._Controls_regions.bed has changed
Binary file iwtomics/example/._DESCRIPTION.txt has changed
Binary file iwtomics/example/._Elements1_regions.bed has changed
Binary file iwtomics/example/._Elements2_regions.bed has changed
Binary file iwtomics/example/._Elements3_regions.bed has changed
Binary file iwtomics/example/._Feature1.bed has changed
Binary file iwtomics/example/._Feature2.bed has changed
Binary file iwtomics/example/._features.header.bed.txt has changed
Binary file iwtomics/example/._regions.header.txt has changed
--- a/iwtomics/example/Controls_regions.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-chr1	91399892	91499892
-chr1	116447079	116547079
-chr2	231381109	231481109
-chr3	47386633	47486633
-chr3	99195712	99295712
-chr3	116765114	116865114
-chr3	134345017	134445017
-chr4	68064019	68164019
-chr4	137465811	137565811
-chr4	173293016	173393016
-chr5	59044110	59144110
-chr5	94592763	94692763
-chr5	108436006	108536006
-chr5	110836898	110936898
-chr5	146661073	146761073
-chr6	99727306	99827306
-chr7	88291325	88391325
-chr7	120999784	121099784
-chr8	126860366	126960366
-chr8	127636547	127736547
-chr11	41362564	41462564
-chr11	101741527	101841527
-chr12	15210277	15310277
-chr13	91106037	91206037
-chr13	91518822	91618822
-chr13	98959030	99059030
-chr15	39087176	39187176
-chr17	58542142	58642142
-chr18	12199823	12299823
-chr20	8173704	8273704
-chr21	16255112	16355112
-chr21	45089115	45189115
-chrX	23898983	23998983
-chrX	37029585	37129585
-chrX	103593349	103693349
--- a/iwtomics/example/DESCRIPTION.txt	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", 
-corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".
--- a/iwtomics/example/Elements1_regions.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-chr2	49960150	50060150
-chr2	55912445	56012445
-chr3	140326750	140426750
-chr4	41772201	41872201
-chr4	70629719	70729719
-chr4	109340735	109440735
-chr5	15025389	15125389
-chr5	43028888	43128888
-chr5	58231354	58331354
-chr5	91277761	91377761
-chr5	119464508	119564508
-chr6	85309170	85409170
-chr6	85762072	85862072
-chr6	134621363	134721363
-chr6	147470164	147570164
-chr7	77195798	77295798
-chr7	77880914	77980914
-chr7	114805399	114905399
-chr10	46350885	46450885
-chr10	67833078	67933078
-chr12	27722692	27822692
-chr12	95518506	95618506
-chr12	117863466	117963466
-chr14	100464166	100564166
-chrX	29266748	29366748
--- a/iwtomics/example/Elements2_regions.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-chr1	65942901	66042901
-chr1	117128102	117228102
-chr1	190338169	190438169
-chr2	227365478	227465478
-chr6	50856764	50956764
-chr6	135703067	135803067
-chr7	38228726	38328726
-chr7	51115898	51215898
-chr7	150325760	150425760
-chr8	25475691	25575691
-chr9	73374609	73474609
-chr11	55092625	55192625
-chr11	86581661	86681661
-chr12	12795284	12895284
-chr12	48151882	48251882
-chr12	83109951	83209951
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--- a/iwtomics/example/Elements3_regions.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
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--- a/iwtomics/example/Feature1.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/iwtomics/example/Feature2.bed	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/iwtomics/example/features.header.bed.txt	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Feature1.bed	ftr1	Feature 1
-Feature2.bed	ftr2	Feature 2
\ No newline at end of file
--- a/iwtomics/example/regions.header.txt	Wed May 31 11:06:30 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Elements1_regions.bed	elem1	Elements 1
-Elements2_regions.bed	elem2	Elements 2
-Elements3_regions.bed	elem3	Elements 3
-Controls_regions.bed	control	Controls
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.R	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,146 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  require(tools,quietly = FALSE)
+  args=commandArgs(TRUE)
+
+  for (i in seq_along(args)) {
+    message(args[[i]])
+  }
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  outrdata=args_values$outrdata
+  outregions=args_values$outregions
+  outfeatures=args_values$outfeatures
+  outpdf=args_values$outpdf
+  regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
+  if("regionsheaderfile" %in% args_names){
+    # the file regionsheaderfile must contain as first column the (unique) regionsfilenames, 
+    # as second column the corresponding ids and as third column the names
+    tryCatch({
+      regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+      regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
+      if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
+        quit(save="no", status=11)
+        stop('Not all regionsfilenames are present in the first column of regionsheader.')
+      }
+      id_regions=regionsheader[regionsfilenames,1]
+      name_regions=regionsheader[regionsfilenames,2]
+    }, error = function(err) {
+      quit(save="no", status=10) #error on header file
+      stop(err)
+    })
+  }else{
+    eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
+    id_regions=paste0('data_',regionsgalaxyids)
+    name_regions=paste0('data_',regionsgalaxyids)
+  }
+  featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
+  if("featuresheaderfile" %in% args_names){
+    # the file featuresheaderfile must contain as first column the (unique) featuresfilenames, 
+    # as second column the corresponding ids and as third column the names
+    tryCatch({
+      featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+      featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
+      if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
+        quit(save="no", status=21)
+        stop('Not all featuresfilenames are present in the first column of featuresheader.')
+      }
+      id_features=featuresheader[featuresfilenames,1]
+      name_features=featuresheader[featuresfilenames,2]
+    }, error = function(err) {
+      quit(save="no", status=20) #error on header file
+      stop(err)
+    })
+  }else{
+    eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
+    id_features=paste0('data_',featuresgalaxyids)
+    name_features=paste0('data_',featuresgalaxyids)
+  }
+  # read parameters (from smoothing on)
+  i_smoothing=which(args_names=='smoothing')
+  for(i in i_smoothing:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load data
+  tryCatch({
+    regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
+                                id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
+  }, error = function(err) {
+    if(grepl('invalid format',err$message)){
+      quit(save="no", status=31) # error, not enough columns in input file
+    }else if(grepl('duplicated regions',err$message)){
+      quit(save="no", status=32) # error, duplicated regions in region file
+    }else if(grepl('duplicated windows',err$message)){
+      quit(save="no", status=33) # error, duplicated windows in feature file
+    }else if(grepl('overlapping windows',err$message)){
+      quit(save="no", status=34) # error, overlapping windows in feature file
+    }else if(grepl('not all regions in datasets',err$message)){
+      quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
+    }else if(grepl('ifferent size windows',err$message)){
+      quit(save="no", status=36) # error, all windows in a feature files must have the same size
+    }
+    #error loading data
+
+    stop(err)
+
+    quit(save="no", status=30)
+    
+ })
+  
+  # smooth data
+  if(smoothing!='no'){
+    tryCatch({
+      if(smoothing=='locpoly'){
+        dist_knots=10
+      }else if(smoothing=='kernel'){
+        degree=3
+        dist_knots=10
+      }else if(smoothing=='splines'){
+        bandwidth=5
+      }
+      if(alignment=='scale'){
+        if(scale==0){
+          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+        }else{
+          regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                                bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
+        }
+      }else{
+        regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+                              bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+      }
+    }, error = function(err) {
+      quit(save="no", status=40) #error on smoothing
+      stop(err)
+    })
+  }
+  
+  # plot data
+  pdf(outpdf,width=10,height=8)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+  dev.off()
+  
+  # create output
+  #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
+              #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
+              #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  save(regionsFeatures,file=outrdata)
+}else{
+  quit(save="no", status=255)
+  stop("Missing IWTomics package")
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.xml	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,325 @@
+<tool id="loadandplot" name="IWTomics Load" version="@VERSION@.0">
+  <description>Smooth and Plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio>
+    <exit_code range="255" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="An error has occurred reading the header file for regions. Please try again." />
+    <exit_code range="11" source="both" level="fatal" description="Not all region files are present in the first column of header file for regions." />
+    <exit_code range="20" source="both" level="fatal" description="An error has occurred reading the header file for features. Please try again." />
+    <exit_code range="21" source="both" level="fatal" description="Not all feature files are present in the first column of header file for features." />
+    <exit_code range="30" source="both" level="fatal" description="An error has occurred reading the data. Please try again." />
+    <exit_code range="31" source="both" level="fatal" description="Not enough columns in input file." />
+    <exit_code range="32" source="both" level="fatal" description="Duplicated regions in region file." />
+    <exit_code range="33" source="both" level="fatal" description="Duplicated windows in feature file." />
+    <exit_code range="34" source="both" level="fatal" description="Overlapping windows in feature file." />
+    <exit_code range="35" source="both" level="fatal" description="Windows in feature files do not cover all regions in region files." />
+    <exit_code range="36" source="both" level="fatal" description="All windows in a feature file must have the same size." />
+    <exit_code range="40" source="both" level="fatal" description="An error has occurred smoothing the data. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+  <command>
+<![CDATA[
+    Rscript $__tool_directory__/loadandplot.R outrdata="${outrdata}" outregions="${outregions}" outfeatures="${outfeatures}" outpdf="${outpdf}"
+
+      #set region_paths = '"\\|"'.join( [ str( $r ) for $r in $regions ] )
+      regionspaths="${region_paths}"
+      #set region_galaxyids = '","'.join( [ str( $r.hid ) for $r in $regions ] )
+      regionsgalaxyids="c(${region_galaxyids})"
+      #set region_names = '"\\|"'.join( [ str( $r.name ) for $r in $regions ] )
+      regionsfilenames="${region_names}"
+      #set region_header = '"\\|"'.join( [ str( $rh.regionsheader ) for $rh in $regionsheaderrepeat ] )
+      #if $region_header != "":
+        regionsheaderfile="${region_header}"
+      #end if
+
+      #set feature_paths = '"\\|"'.join( [ str( $f ) for $f in $features ] )
+      featurespaths="${feature_paths}"
+      #set feature_galaxyids = '","'.join( [ str( $f.hid ) for $f in $features ] )
+      featuresgalaxyids="c(${feature_galaxyids})"
+      #set feature_names = '"\\|"'.join( [ str( $f.name ) for $f in $features ] )
+      featuresfilenames="${feature_names}"
+      #set feature_header = '"\\|"'.join( [ str( $fh.featuresheader ) for $fh in $featuresheaderrepeat ] )
+      #if $feature_header != "":
+        featuresheaderfile="${feature_header}"
+      #end if
+
+      smoothing="'${conditionaltype.smoothing}'"
+      start.are.0based="${zerobased}"
+      #if $conditionaltype.smoothing == 'no':
+        alignment="'${conditionaltype.alignment}'"
+      #elif $conditionaltype.smoothing == 'locpoly':
+        alignment="'${conditionaltype.locpolyconditionalscale.alignment}'"
+        #if $conditionaltype.locpolyconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.locpolyconditionalscale.scalegrid}"
+        #end if
+        bandwidth="${conditionaltype.locpolybandwidth}"
+        degree="${conditionaltype.locpolydegree}"
+        fill_gaps="${conditionaltype.fillgaps}"
+      #elif $conditionaltype.smoothing == 'kernel':
+        alignment="'${conditionaltype.kernelconditionalscale.alignment}'"
+        #if $conditionaltype.kernelconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.kernelconditionalscale.scalegrid}"
+        #end if
+        bandwidth="${conditionaltype.kernelbandwidth}"
+        fill_gaps="${conditionaltype.fillgaps}"
+      #elif $conditionaltype.smoothing == 'splines':
+        alignment="'${conditionaltype.splinesconditionalscale.alignment}'"
+        #if $conditionaltype.splinesconditionalscale.alignment == 'scale':
+          scale="${conditionaltype.splinesconditionalscale.scalegrid}"
+        #end if
+        degree="${conditionaltype.splinesdegree}"
+        dist_knots="${conditionaltype.splinesdistknots}"
+        fill_gaps="${conditionaltype.fillgaps}"
+      #end if
+
+      average="${plotres.average}"
+      size="${plotres.size}"
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
+        #else:
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+        #end if
+      #end if
+
+      >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"
+    -->
+  </command>
+
+  <inputs>
+    <!-- regions -->
+    <param format="tabular" name="regions" type="data" label="Select region files" multiple="true" help="" />
+    <repeat name="regionsheaderrepeat" title="Header file for regions (optional)" min="0" max="1" help="Tabular file. Column 1: names of the region files; Column 2: unique identifiers of the region datasets (spaces and special characters are not allowed); Column 3: name of the region datasets to be used in the output.">
+      <param format="tabular" name="regionsheader" type="data" label="Select header file" />
+    </repeat>
+
+    <!-- features -->
+    <param format="tabular" name="features" type="data" label="Select feature files" multiple="true" help="" />
+    <repeat name="featuresheaderrepeat" title="Header file for features (optional)" min="0" max="1" help="Tabular file. Column 1: names of the feature files; Column 2: unique identifiers of the features (spaces and special characters are not allowed); Column 3: name of the features to be used in the output.">
+      <param format="tabular" name="featuresheader" type="data" label="Select header file" />
+    </repeat>
+
+    <!-- zero-base one-base -->
+    <param name="zerobased" type="select" label="Start positions are:" multiple="false" help="">
+      <option value="TRUE">0-based</option>
+      <option value="FALSE">1-based</option>
+    </param>
+
+    <!-- conditional smoothing -->
+    <conditional name="conditionaltype">
+      <!-- smoothing -->
+      <param name="smoothing" type="select" label="Smoothing" help="Type of smoothing to be applied to the feature curves.">
+        <option value="no">No</option>
+        <option value="locpoly">Local Polynomials</option>
+        <option value="kernel">Gaussian Kernel</option>
+        <option value="splines">B-Splines</option>
+      </param>
+      <!-- conditional choice: smoothing=no -->
+      <when value="no">
+        <param name="alignment" type="select" label="Region alignment" help="">
+          <option value="center">Center - Alignment on the central position</option>
+          <option value="left">Left - Alignment on the starting position</option>
+          <option value="right">Right - Alignment on the ending position</option>
+        </param>
+      </when>
+      <!-- conditional choice: smoothing=locpoly -->
+      <when value="locpoly">
+        <!-- conditional region alignment -->
+        <conditional name="locpolyconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+        <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+      <!-- conditional choice: smoothing=kernel -->
+      <when value="kernel">
+        <!-- conditional region alignment -->
+        <conditional name="kernelconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+      <!-- conditional choice: smoothing=splines -->
+      <when value="splines">
+        <!-- conditional region alignment -->
+        <conditional name="splinesconditionalscale">
+          <param name="alignment" type="select" label="Region alignment" help="">
+            <option value="center">Center - Alignment on the central position</option>
+            <option value="left">Left - Alignment on the starting position</option>
+            <option value="right">Right - Alignment on the ending position</option>
+            <option value="scale">Scale - Scaling all regions to the same length</option>
+          </param>
+          <when value="scale">
+            <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />
+          </when>
+        </conditional>
+
+        <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />
+        <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />
+
+        <!-- fill gaps -->
+        <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />
+      </when>
+    </conditional>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot data" expanded="True">
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />
+      <!-- sample size in each position -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type" help="">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.loadandplot.stackerr.txt" from_work_dir="iwtomics.loadandplot.stackerr.txt" />-->
+    <data format="rdata" name="outrdata" label="${tool.name} on ${on_string}: IWTomicsData Object" from_work_dir="iwtomics.loadandplot.RData" />
+    <data format="tabular" name="outregions" label="${tool.name} on ${on_string}: Region Dataset IDs" from_work_dir="iwtomics.loadandplot.regions.txt" />
+    <data format="tabular" name="outfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.loadandplot.features.txt" />
+    <data format="pdf" name="outpdf" label="${tool.name} on ${on_string}: Plotted Data" from_work_dir="iwtomics.loadandplot.pdf" />
+  </outputs>
+
+  <help>
+This tool imports a collection of genomic region datasets, and associates to each region
+multiple genomic feature measurements. It allows to align the regions in multiple ways
+(center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
+measurements) and to create a graphical representation of the feature measurements in each
+region datasets (aligned curves or pointwise quantile curves).
+
+-----
+
+**Region datasets**
+
+Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
+start end (extra columns present in the input file are ignored). Regions can be of different
+length::
+
+    chr2  49960150  50060150
+    chr2  55912445  56012445
+    ...
+
+-----
+
+**Feature measurements**
+
+Feature measurements corresponding to all the regions can be provided as a BED or Tabular
+file with tab delimited columns chr start end value::
+
+    chr2  49960150  49962150  0.9426
+    chr2  49962150  49964150  0.7816
+    ...
+
+Each feature must be measured in windows of a fixed size inside all the regions (missing
+values must be indicated as NA). Another way to import feature measurements is from a
+Tabular file with the first three columns chr start end corresponding to the different genomic
+regions, followed on the same row by all the measurements in fixed-size windows::
+
+    chr2  49960150  50060150  0.9426  0.7816  0.8921  ...  ...  1.2063
+    chr2  55912445  56012445  0.8719  0.9975  1.1619  ...  ...  0.9601
+    ...
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
+2. Region dataset identifiers;
+3. Feature identifiers;
+4. PDF file with the plotted data.
+
+1-3 can be used as input of the tool *IWTomics Test and Plot*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{
+               iwt-functional-data,
+               author = {Pini, Alessia and Vantini, Simone},
+               title = {Interval-Wise Testing for functional data},
+               journal = {Journal of Nonparametric Statistics},
+               year = {2017},
+               volume = {29},
+               number = {2},
+               pages = {407-424}
+      }
+    </citation>
+    <citation type="bibtex">
+      @MANUAL{
+               iwtomics,
+               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+               title = {IWTomics: Interval-Wise Testing for Omics Data},
+               note = {R package version 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,9 @@
+<macros>
+    <token name="@VERSION@">1.0.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.3.1">R</requirement>
+            <requirement type="package" version="@VERSION">bioconductor-iwtomics</requirement>
+        </requirements>
+    </xml>
+</macros>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.R	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,117 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  adjustedpvalue=args_values$adjustedpvalue
+  iwtomicsrespdf=args_values$iwtomicsrespdf
+  iwtomicssumpdf=args_values$iwtomicssumpdf
+  iwtomicsrdata=args_values$iwtomicsrdata
+  iwtomicstests=args_values$iwtomicstests
+  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+  test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
+  feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
+  # read parameters (from test_subset on)
+  i_scale_subset=which(args_names=='scale_subset')
+  for(i in i_scale_subset:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load RData
+  load(iwtomicsrdata)
+  # read testids and featureids and check them
+  unlisted=lapply(seq_along(test_subset),
+                   function(i){
+                     test_subset_i=eval(parse(text=test_subset[i]))
+                     feature_subset_i=eval(parse(text=feature_subset[i]))
+                     test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
+                     feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
+                     scale_subset_i=rep(scale_subset[i],length(test_subset_i))
+                     return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
+                   })
+  test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
+  feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
+  scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
+  testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  id_features_subset=featureids[feature_subset]
+  if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
+    quit(save="no", status=10)
+    stop('Wrong test ids')
+  }
+  if(sum(featureids!=idFeatures(regionsFeatures_test))){
+    quit(save="no", status=20)
+    stop('Wrong feature ids')
+  }
+  # retrieve test and features_subset ids
+  id_features_subset=featureids[feature_subset]
+  if(sum(duplicated(paste0(test_subset,id_features_subset)))){
+    quit(save="no", status=30)
+    stop('Two scale thresholds selected for the same test and feature.')
+  }
+  # If scale_subset=0, do not change the threshold
+  default=(scale_subset==0)
+  scale_subset=scale_subset[!default]
+  test_subset=test_subset[!default]
+  id_features_subset=id_features_subset[!default]
+  
+  # get scale threshold
+  scale_threshold=lapply(regionsFeatures_test@test$result,
+                         function(result) unlist(lapply(result,function(feature) feature$max_scale)))
+  for(i in seq_along(test_subset)){
+    if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
+      quit(save="no", status=40)
+      stop('Scale threshold too high.')
+    }
+    scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
+  }
+  
+  # create adjustedvalue output
+  pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold)
+  for(test in seq_along(pval)){
+    for(id_feature in idFeatures(regionsFeatures_test)){
+      write(paste0('Test: ',testids[test],', on feature ',id_feature),
+              file=adjustedpvalue,append=TRUE,sep='\t')
+        pval_i=as.data.frame(t(pval[[test]][[id_feature]]))
+        row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]])
+        write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+        write('',file=adjustedpvalue,append=TRUE,sep='\t')
+      }
+    }
+  
+  
+  # plot test results
+  pdf(iwtomicsrespdf,width=5,height=7)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE)
+  dev.off()
+  
+  # plot summary results
+  if(groupby!='none'){
+    tryCatch({
+      pdf(iwtomicssumpdf,width=15,height=10)
+      plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
+      dev.off()
+    }, error = function(err) {
+      if (grepl('selected features with different resolution',err$message)) {
+        quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
+        stop(err)
+      }
+      quit(save="no", status=60) #error 
+      stop(err)
+    })
+  }
+  
+}else{
+  quit(save="no", status=255)
+  stop("Missing IWTomics package")
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.xml	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,201 @@
+<tool id="plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
+  <description>on Test Scale</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio>
+    <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="Wrong test ids." />
+    <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
+    <exit_code range="30" source="both" level="fatal" description="Two scale thresholds selected for the same test and feature." />
+    <exit_code range="40" source="both" level="fatal" description="Scale threshold too high." />
+    <exit_code range="50" source="both" level="fatal" description="Group by 'test' but selected features with different resolution." />
+    <exit_code range="60" source="both" level="fatal" description="Summary plot error. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+  <command>
+<![CDATA[
+    Rscript $__tool_directory__/plotwithscale.R adjustedpvalue="${adjustedpvalue}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}"
+      iwtomicsrdata="${rdata}"
+      iwtomicstests="${testids}"
+      iwtomicsselectedfeatures="${featureids}"
+
+      #set test_subset = '"\\|"'.join( [ str( $e.test ) for $e in $scalesection.thresholdontestscale ] )
+      test_subset="${test_subset}"
+      #set feature_subset = '"\\|"'.join( [ str( $e.feature ) for $e in $scalesection.thresholdontestscale ] )
+      feature_subset="${feature_subset}"
+      #set scale_subset = '","'.join( [ str( $e.scale ) for $e in $scalesection.thresholdontestscale ] )
+      scale_subset="c(${scale_subset})"
+
+      testalpha="${plotres.alpha}"
+      average="${plotres.average}"
+      size="${plotres.size}"
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
+        #else:
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+        #end if
+      #end if
+
+      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      #if $plotsum.conditionalgroupby.groupby == "test":
+        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
+        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+      #elif $plotsum.conditionalgroupby.groupby == "feature":
+        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
+        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+      #end if
+
+      >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"
+    -->
+  </command>
+
+  <inputs>
+    <help>
+    ...
+    </help>
+
+    <!-- RData -->
+    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
+    <!-- test IDs -->
+    <param format="tabular" name="testids" type="data" label="Select test IDs" help="File created by 'IWTomics Test and Plot'." />
+    <!-- feature IDs -->
+    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Test and Plot'." />
+
+    <!-- repeat threshold on test scale -->
+    <section name="scalesection" title="Select scale for Interval-Wise Testing and plot" expanded="True" help="Maximum interval length for the p-value adjustment. If 0 the maximum possible scale is used.">
+      <repeat name="thresholdontestscale" title="Threshold on test scale" min="1">
+        <param name="test" type="data_column" data_ref="testids" numerical="False" label="Test ID" multiple="True" use_header_names="True" />
+        <param name="feature" type="data_column" data_ref="featureids" numerical="False" label="Feature ID" multiple="True" use_header_names="True" />
+        <param name="scale" type="integer" value="0" min="0" label="Scale" />
+      </repeat>
+    </section>
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot IWTomics test results" expanded="True">
+      <!-- alpha -->
+      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
+      <!-- average -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+
+    <!-- summary plot -->
+    <section name="plotsum" title="Summary plot" expanded="True">
+      <!-- conditional group by -->
+      <conditional name="conditionalgroupby">
+        <!-- group by -->
+        <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
+          <option value="none">No plot</option>
+          <option value="test">Group by test</option>
+          <option value="feature">Group by feature</option>
+        </param>
+        <when value="test">
+          <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+        <when value="feature">
+          <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
+    <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.testandplot.adjustedpvalue.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
+  </outputs>
+
+  <help>
+This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
+for the different tests performed at the selected scale, and it creates a graphical representation of the
+Interval-Wise Testing results and a summary plot (optional) at the selected scale.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
+These files are created by the tool *IWTomics Test and Plot*.
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot.
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{
+               iwt-functional-data,
+               author = {A Pini and S. Vantini},
+               title = {Interval-Wise Testing for functional data},
+               journal = {Journal of Nonparametric Statistics},
+               year = {2017},
+               volume = {29},
+               number = {2},
+               pages = {407-424}
+      }
+    </citation>
+    <citation type="bibtex">
+      @MANUAL{
+               iwtomics,
+               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+               title = {IWTomics: Interval-Wise Testing for Omics Data},
+               note = {R package version 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.R	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,99 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+  args=commandArgs(TRUE)
+  
+  # get args names and values
+  args_values=strsplit(args,'=')
+  args_names=unlist(lapply(args_values,function(arg) arg[1]))
+  names(args_values)=args_names
+  args_values=lapply(args_values,function(arg) arg[2])
+  # read filenames
+  adjustedpvaluematrix=args_values$adjustedpvaluematrix
+  iwtomicsrespdf=args_values$iwtomicsrespdf
+  iwtomicssumpdf=args_values$iwtomicssumpdf
+  regionids=args_values$regionids
+  featureids=args_values$featureids
+  rdatafile=args_values$rdatafile
+  iwtomicsrdata=args_values$iwtomicsrdata
+  iwtomicstests=args_values$iwtomicstests
+  iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+  # read parameters (from region1 on)
+  i_region1=which(args_names=='region1')
+  for(i in i_region1:length(args)){
+    eval(parse(text=args[[i]]))
+  }
+  
+  # load RData
+  load(rdatafile)
+  # read regionids and featureids
+  regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+  # retrieve region1, region2 and features_subset ids and check they are in the RData
+  id_region1=regionids[region1]
+  id_region2=regionids[region2]
+  id_features_subset=featureids[features_subset]
+  if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
+    quit(save="no", status=10)
+    stop('Wrong region ids')
+  }
+  if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
+    quit(save="no", status=20)
+    stop('Wrong feature ids')
+  }
+  if(sum(duplicated(paste0(id_region1,id_region2)))){
+    quit(save="no", status=30)
+    stop('Same test repeated multiple times.')
+  }
+  
+  # perform test
+  tryCatch({
+    # fix repeated probs
+    if(statistics=='quantile'){
+      # fix repeated probs
+      testprobs=sort(unique(testprobs))
+    }else{
+      testprobs=0.5
+    }
+    regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
+                                      statistics=statistics,probs=testprobs,B=B)
+    # create adjustedvaluematrix output
+    for(test in seq_along(id_region1)){
+      for(id_feature in id_features_subset){
+        write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
+              file=adjustedpvaluematrix,append=TRUE,sep='\t')
+        pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
+        row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
+        write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+        write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
+      }
+    }
+  }, error = function(err) {
+    quit(save="no", status=40) #error testing
+    stop(err)
+  })
+  
+  # plot test results
+  pdf(iwtomicsrespdf,width=5,height=7)
+  if(plottype=='boxplot'){
+    # fix repeated probs
+    probs=sort(unique(probs))
+  }else{
+    probs=c(0.25,0.5,0.75)
+  }
+  plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+  dev.off()
+  
+  # plot summary results
+  if(groupby!='none'){
+    pdf(iwtomicssumpdf,width=15,height=10)
+    plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
+    dev.off()
+  }
+  
+  # create output
+  write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+  save(regionsFeatures_test,file=iwtomicsrdata)
+}else{
+  quit(save="no", status=255)
+  stop("Missing IWTomics package")
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.xml	Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,239 @@
+<tool id="testandplot" name="IWTomics Test" version="@VERSION@.0">
+  <description>and Plot</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio>
+    <exit_code range="-1" source="both" level="fatal" description="Missing IWTomics package. Please be sure to have it installed before using this tool." />
+    <exit_code range="10" source="both" level="fatal" description="Wrong region ids." />
+    <exit_code range="20" source="both" level="fatal" description="Wrong feature ids." />
+    <exit_code range="30" source="both" level="fatal" description="Same test repeated multiple times." />
+    <exit_code range="40" source="both" level="fatal" description="Testing error." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
+  </stdio>
+
+  <command>
+<![CDATA[
+    Rscript $__tool_directory__/testandplot.R adjustedpvaluematrix="${adjustedpvaluematrix}" iwtomicsrespdf="${iwtomicsrespdf}" iwtomicssumpdf="${iwtomicssumpdf}" iwtomicsrdata="${iwtomicsrdata}" iwtomicstests="${iwtomicstests}" iwtomicsselectedfeatures="${iwtomicsselectedfeatures}"
+      regionids="${regionids}"
+      featureids="${featureids}"
+      rdatafile="${rdata}"
+
+      #set region1 = '","'.join( [ str( $r.region0 ) for $r in $regionssection.regions ] )
+      #set region2 = '","'.join( [ str( $r.region1 ) for $r in $regionssection.regions ] )
+      region1="c(${region1})"
+      region2="c(${region2})"
+
+      features_subset="c(${featureslist})"
+
+      statistics="'${conditionalstatistics.statistics}'"
+      #if $conditionalstatistics.statistics == "quantile":
+        #set probabilities = '","'.join( [ str( $p.qprob ) for $p in $conditionalstatistics.quantilesection.qprobabilities ] )
+        testprobs="c(${probabilities})"
+      #end if
+
+      B="${permutations}"
+
+      testalpha="${plotres.alpha}"
+      average="${plotres.average}"
+      size="${plotres.size}"
+      plottype="'${plotres.conditionalplottype.plottype}'"
+      #if $plotres.conditionalplottype.plottype == 'boxplot':
+        #set probs = '","'.join( [ str( $p.prob ) for $p in $plotres.conditionalplottype.probabilitiessection.probabilities ] )
+        #if $probs != "":
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2},${probs})"
+        #else:
+          probs="c(${plotres.conditionalplottype.probabilitiessection.prob0},${plotres.conditionalplottype.probabilitiessection.prob1},${plotres.conditionalplottype.probabilitiessection.prob2})"
+        #end if
+      #end if
+
+      groupby="'${plotsum.conditionalgroupby.groupby}'"
+      #if $plotsum.conditionalgroupby.groupby == "test":
+        summaryalpha="${plotsum.conditionalgroupby.testalphaplot}"
+        only_significant="${plotsum.conditionalgroupby.testonlysig}"
+      #elif $plotsum.conditionalgroupby.groupby == "feature":
+        summaryalpha="${plotsum.conditionalgroupby.featurealphaplot}"
+        only_significant="${plotsum.conditionalgroupby.featureonlysig}"
+      #end if
+
+     >& /dev/null
+]]>
+    <!--
+    to print the stack add the following line at the end of the command and enable the corresponding entry in output
+    2> "${stackerr}"
+    -->
+  </command>
+
+  <inputs>
+    <!-- RData -->
+    <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
+    <!-- region IDs -->
+    <param format="tabular" name="regionids" type="data" label="Select region dataset IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
+    <!-- feature IDs -->
+    <param format="tabular" name="featureids" type="data" label="Select feature IDs" help="File created by 'IWTomics Load Smooth and Plot'." />
+
+    <!-- repeat region ids -->
+    <section name="regionssection" title="Select regions for Interval-Wise Testing" expanded="True" help="IDs of the region datasets to be tested.">
+      <repeat name="regions" title="Two-sample test" min="1">
+        <param name="region0" type="data_column" data_ref="regionids" numerical="False" label="Region 1" multiple="False" use_header_names="True" />
+        <param name="region1" type="data_column" data_ref="regionids" numerical="False" label="Region 2" multiple="False" use_header_names="True" />
+      </repeat>
+    </section>
+
+    <!-- feature ids list -->
+    <param name="featureslist" type="data_column" data_ref="featureids" numerical="False" label="Select features" multiple="True" use_header_names="True" help="IDs of the features to be tested." />
+
+    <!-- conditional statistics -->
+    <conditional name="conditionalstatistics">
+      <!-- statistics -->
+      <param name="statistics" type="select" label="Test statistics">
+        <option value="mean">Mean difference</option>
+        <option value="median">Median difference</option>
+        <option value="variance">Variance ratio</option>
+        <option value="quantile">Quantile difference(s)</option>
+      </param>
+      <!-- conditional choice: statistics=quantile -->
+      <when value="quantile">
+        <section name="quantilesection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantiles in test statistics.">
+          <repeat name="qprobabilities" title="Probabilities" min="1">
+            <param name="qprob" size="4" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+          </repeat>
+        </section>
+      </when>
+    </conditional>
+
+    <!-- permutations -->
+    <param name="permutations" type="integer" value="1000" min="1" label="Number of permutations" />
+
+    <!-- plot IWTomics results -->
+    <section name="plotres" title="Plot IWTomics test results" expanded="True">
+      <!-- alpha -->
+      <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+      <!-- average -->
+      <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
+      <!-- average -->
+      <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
+      <!-- conditional plot type -->
+      <conditional name="conditionalplottype">
+        <!-- plot type -->
+        <param name="plottype" type="select" label="Plot type">
+          <option value="boxplot">Pointwise quantile curves (boxplot)</option>
+          <option value="curves">Curves (aligned)</option>
+        </param>
+        <!-- conditional choice: plottype=boxplot -->
+        <when value="boxplot">
+          <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
+            <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
+            <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
+            <repeat name="probabilities" title="Probabilities">
+              <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
+            </repeat>
+          </section>
+        </when>
+      </conditional>
+    </section>
+
+    <!-- summary plot -->
+    <section name="plotsum" title="Summary plot" expanded="True">
+      <!-- conditional group by -->
+      <conditional name="conditionalgroupby">
+        <!-- group by -->
+        <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
+          <option value="none">No plot</option>
+          <option value="test">Group by test</option>
+          <option value="feature">Group by feature</option>
+        </param>
+        <when value="test">
+          <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+        <when value="feature">
+          <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
+          <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
+        </when>
+      </conditional>
+    </section>
+  </inputs>
+
+  <outputs>
+    <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
+    <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
+    <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
+    <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
+    <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
+    <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />
+    <data format="tabular" name="iwtomicsselectedfeatures" label="${tool.name} on ${on_string}: Feature IDs" from_work_dir="iwtomics.testandplot.selectedfeatures.txt" />
+  </outputs>
+
+  <help>
+This tool statistically evaluates differences in genomic features between groups of regions along the genome.
+In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
+Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
+tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
+and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
+and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
+permits to select the scale to be used in the plots.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
+These files are created by the tool *IWTomics Load Smooth and Plot*.
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot;
+4. RData with the IWTomicsData object with the test results;
+5. Test identifiers;
+6. Feature identifiers.
+
+4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @ARTICLE{
+               iwt-functional-data,
+               author = {A Pini and S. Vantini},
+               title = {Interval-Wise Testing for functional data},
+               journal = {Journal of Nonparametric Statistics},
+               year = {2017},
+               volume = {29},
+               number = {2},
+               pages = {407-424}
+      }
+    </citation>
+    <citation type="bibtex">
+      @MANUAL{
+               iwtomics,
+               author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+               title = {IWTomics: Interval-Wise Testing for Omics Data},
+               note = {R package version 0.99.12},
+               year = {2017}
+      }
+    </citation>
+  </citations>
+
+</tool>