# HG changeset patch
# User proteore
# Date 1518770236 18000
# Node ID 760470ddb9ca47d5e34717cf343d51d74691ba8f
# Parent  9d4f20618ab4fe07385f2b3b7901c2e6f3f8e1fd
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty

diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/Bredberg.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Bredberg.txt	Fri Feb 16 03:37:16 2018 -0500
@@ -0,0 +1,121 @@
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/DESeq.txt
--- a/test-data/DESeq.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1249 +0,0 @@
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/FQ.txt
--- a/test-data/FQ.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1092 +0,0 @@
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ID_Converter_FKW_Lacombe_et_al_2017_OK.txt	Fri Feb 16 03:37:16 2018 -0500
@@ -0,0 +1,152 @@
+Protein accession number (UniProt)	Protein name	Number of peptides (razor + unique)	neXtProt_ID	UniProt.ID	GeneID	MIM	Ensembl
+P15924	Desmoplakin	69	NX_P15924	DESP_HUMAN	1832	125647; 605676; 607450; 607655; 609638; 612908; 615821	ENSG00000096696
+P02538	Keratin, type II cytoskeletal 6A	53	NX_P02538	K2C6A_HUMAN	3853	148041; 615726	ENSG00000205420
+P02768	Serum albumin	44	NX_P02768	ALBU_HUMAN	213	103600; 615999; 616000	ENSG00000163631
+P08779	Keratin, type I cytoskeletal 16	29	NX_P08779	K1C16_HUMAN	3868	148067; 167200; 613000	ENSG00000186832
+Q02413	Desmoglein-1	24	NX_Q02413	DSG1_HUMAN	1828	125670; 148700; 615508	ENSG00000134760
+P07355	Annexin A2;Putative annexin A2-like protein	22	NX_P07355	ANXA2_HUMAN	302	151740	ENSG00000182718
+P14923	Junction plakoglobin	22	NX_P14923	PLAK_HUMAN	3728	173325; 601214; 611528	ENSG00000173801
+P02788	Lactotransferrin	21	NX_P02788	TRFL_HUMAN	4057	150210	ENSG00000012223
+Q9HC84	Mucin-5B	21	NX_Q9HC84	MUC5B_HUMAN	727897	178500; 600770	ENSG00000117983
+P29508	Serpin B3	20	NX_P29508	SPB3_HUMAN	6317	600517	ENSG00000057149
+P63261	Actin, cytoplasmic 2	19	NX_P63261	ACTG_HUMAN	71	102560; 604717; 614583	ENSG00000184009
+Q8N1N4	Keratin, type II cytoskeletal 78	18	NX_Q8N1N4	K2C78_HUMAN	196374	611159	ENSG00000170423
+Q04695	Keratin, type I cytoskeletal 17	18	NX_Q04695	K1C17_HUMAN	3872	148069; 167210; 184500	ENSG00000128422
+P01876	Ig alpha-1 chain C region	16	NX_P01876	IGHA1_HUMAN	NA	146900	ENSG00000211895; ENSG00000282633
+Q01469	Fatty acid-binding protein 5, epidermal	15	NX_Q01469	FABP5_HUMAN	2171	605168	ENSG00000164687
+P31944	Caspase-14	15	NX_P31944	CASPE_HUMAN	23581	605848; 617320	ENSG00000105141
+P01833	Polymeric immunoglobulin receptor	15	NX_P01833	PIGR_HUMAN	5284	173880	ENSG00000162896
+P06733	Alpha-enolase	15	NX_P06733	ENOA_HUMAN	2023	172430	ENSG00000074800
+P25311	Zinc-alpha-2-glycoprotein	15	NX_P25311	ZA2G_HUMAN	563	194460	ENSG00000160862
+Q15149	Plectin	15	NX_Q15149	PLEC_HUMAN	5339	131950; 226670; 601282; 612138; 613723; 616487	ENSG00000178209
+P19013	Keratin, type II cytoskeletal 4	13	NX_P19013	K2C4_HUMAN	NA	123940; 193900	ENSG00000170477
+Q6KB66	Keratin, type II cytoskeletal 80	13	NX_Q6KB66	K2C80_HUMAN	144501	611161	ENSG00000167767
+Q08188	Protein-glutamine gamma-glutamyltransferase E	12	NX_Q08188	TGM3_HUMAN	7053	600238; 617251	ENSG00000125780
+P13646	Keratin, type I cytoskeletal 13	11	NX_P13646	K1C13_HUMAN	3860	148065; 615785	ENSG00000171401
+Q86YZ3	Hornerin	11	NX_Q86YZ3	HORN_HUMAN	388697	616293	ENSG00000197915
+P04259	Keratin, type II cytoskeletal 6B	10	NX_P04259	K2C6B_HUMAN	3854	148042; 615728	ENSG00000185479
+P02545	Prelamin-A/C;Lamin-A/C	10	NX_P02545	LMNA_HUMAN	4000	115200; 150330; 151660; 159001; 176670; 181350; 212112; 248370; 275210; 605588; 610140; 613205; 616516	ENSG00000160789
+P04083	Annexin A1	10	NX_P04083	ANXA1_HUMAN	301	151690	ENSG00000135046
+P11021	78 kDa glucose-regulated protein	10	NX_P11021	GRP78_HUMAN	3309	138120	ENSG00000044574
+P02787	Serotransferrin	9	NX_P02787	TRFE_HUMAN	7018	190000; 209300	ENSG00000091513
+P04040	Catalase	9	NX_P04040	CATA_HUMAN	847	115500; 614097	ENSG00000121691
+P31151	Protein S100-A7	9	NX_P31151	S10A7_HUMAN	6278	600353	ENSG00000143556
+P31947	14-3-3 protein sigma	9	NX_P31947	1433S_HUMAN	2810	601290	ENSG00000175793
+Q96P63	Serpin B12	9	NX_Q96P63	SPB12_HUMAN	89777	615662	ENSG00000166634
+P14618	Pyruvate kinase PKM	9	NX_P14618	KPYM_HUMAN	5315	179050	ENSG00000067225
+P60174	Triosephosphate isomerase	9	NX_P60174	TPIS_HUMAN	7167	190450; 615512	ENSG00000111669
+Q06830	Peroxiredoxin-1	9	NX_Q06830	PRDX1_HUMAN	5052	176763	ENSG00000117450
+P01040	Cystatin-A	8	NX_P01040	CYTA_HUMAN	1475	184600; 607936	ENSG00000121552
+P05089	Arginase-1	8	NX_P05089	ARGI1_HUMAN	383	207800; 608313	ENSG00000118520
+P01834	Ig kappa chain C region	8	NX_P01834	IGKC_HUMAN	NA	147200; 614102	NA
+P04406	Glyceraldehyde-3-phosphate dehydrogenase	8	NX_P04406	G3P_HUMAN	2597	138400	ENSG00000111640
+P0DMV9	Heat shock 70 kDa protein 1B	8	NX_P0DMV9	HS71B_HUMAN	3303; 3304	140550; 603012	ENSG00000204388; ENSG00000224501; ENSG00000212866; ENSG00000231555; ENSG00000232804
+P13639	Elongation factor 2	8	NX_P13639	EF2_HUMAN	1938	130610; 609306	ENSG00000167658
+P35579	Myosin-9	8	NX_P35579	MYH9_HUMAN	4627	153640; 153650; 155100; 160775; 600208; 603622; 605249	ENSG00000100345
+P68371	Tubulin beta-4B chain	8	NX_P68371	TBB4B_HUMAN	10383	602660	ENSG00000188229
+Q8WVV4	Protein POF1B	8	NX_Q8WVV4	POF1B_HUMAN	79983	300603; 300604	ENSG00000124429
+O75635	Serpin B7	7	NX_O75635	SPB7_HUMAN	8710	603357; 615598	ENSG00000166396
+P01857	Ig gamma-1 chain C region	7	NX_P01857	IGHG1_HUMAN	NA	147100; 254500	ENSG00000211896; ENSG00000277633
+P61626	Lysozyme C	7	NX_P61626	LYSC_HUMAN	4069	105200; 153450	ENSG00000090382
+P68363	Tubulin alpha-1B chain	7	NX_P68363	TBA1B_HUMAN	10376	602530	ENSG00000123416
+P01009	Alpha-1-antitrypsin;Short peptide from AAT	6	NX_P01009	A1AT_HUMAN	5265	107400; 613490	ENSG00000197249
+P07900	Heat shock protein HSP 90-alpha	6	NX_P07900	HS90A_HUMAN	3320	140571	ENSG00000080824
+Q9NZH8	Interleukin-36 gamma	6	NX_Q9NZH8	IL36G_HUMAN	56300	605542	ENSG00000136688
+O43707	Alpha-actinin-4;Alpha-actinin-1	6	NX_O43707	ACTN4_HUMAN	81	603278; 604638	ENSG00000130402; ENSG00000282844
+O75223	Gamma-glutamylcyclotransferase	6	NX_O75223	GGCT_HUMAN	79017	137170	ENSG00000006625
+P00338	L-lactate dehydrogenase A chain	6	NX_P00338	LDHA_HUMAN	3939	150000; 612933	ENSG00000134333
+P07339	Cathepsin D	6	NX_P07339	CATD_HUMAN	1509	116840; 610127	ENSG00000117984
+P62987	Ubiquitin-60S ribosomal protein L40	6	NX_P62987	RL40_HUMAN	7311	191321	ENSG00000221983
+P10599	Thioredoxin	6	NX_P10599	THIO_HUMAN	7295	187700	ENSG00000136810
+Q9UGM3	Deleted in malignant brain tumors 1 protein	6	NX_Q9UGM3	DMBT1_HUMAN	1755	137800; 601969	ENSG00000187908
+Q9UI42	Carboxypeptidase A4	6	NX_Q9UI42	CBPA4_HUMAN	51200	607635	ENSG00000128510
+P47929	Galectin-7	5	NX_P47929	LEG7_HUMAN	3963; 653499	600615; 617139	ENSG00000178934; ENSG00000205076; ENSG00000282902; ENSG00000283082
+Q13867	Bleomycin hydrolase	5	NX_Q13867	BLMH_HUMAN	642	602403	ENSG00000108578
+Q6P4A8	Phospholipase B-like 1	5	NX_Q6P4A8	PLBL1_HUMAN	79887	NA	ENSG00000121316
+O75369	Filamin-B	5	NX_O75369	FLNB_HUMAN	2317	108720; 108721; 112310; 150250; 272460; 603381	ENSG00000136068
+P00441	Superoxide dismutase [Cu-Zn]	5	NX_P00441	SODC_HUMAN	6647	105400; 147450	ENSG00000142168
+P04792	Heat shock protein beta-1	5	NX_P04792	HSPB1_HUMAN	3315	602195; 606595; 608634	ENSG00000106211
+P11142	Heat shock cognate 71 kDa protein	5	NX_P11142	HSP7C_HUMAN	3312	600816	ENSG00000109971
+P58107	Epiplakin	5	NX_P58107	EPIPL_HUMAN	83481	607553	NA
+P60842	Eukaryotic initiation factor 4A-I	5	NX_P60842	IF4A1_HUMAN	1973	602641	ENSG00000161960
+P62937	Peptidyl-prolyl cis-trans isomerase A	5	NX_P62937	PPIA_HUMAN	5478	123840	ENSG00000196262
+P63104	14-3-3 protein zeta/delta	5	NX_P63104	1433Z_HUMAN	7534	601288	ENSG00000164924
+Q92820	Gamma-glutamyl hydrolase	5	NX_Q92820	GGH_HUMAN	8836	601509	ENSG00000137563
+O75342	Arachidonate 12-lipoxygenase, 12R-type	4	NX_O75342	LX12B_HUMAN	242	242100; 603741	ENSG00000179477
+P09211	Glutathione S-transferase P	4	NX_P09211	GSTP1_HUMAN	2950	134660	ENSG00000084207
+P31025	Lipocalin-1	4	NX_P31025	LCN1_HUMAN	3933	151675	ENSG00000160349
+P48594	Serpin B4	4	NX_P48594	SPB4_HUMAN	6318	600518	ENSG00000206073
+Q14574	Desmocollin-3	4	NX_Q14574	DSC3_HUMAN	1825	600271; 613102	ENSG00000134762
+Q5T750	Skin-specific protein 32	4	NX_Q5T750	XP32_HUMAN	100129271	NA	ENSG00000198854
+Q6UWP8	Suprabasin	4	NX_Q6UWP8	SBSN_HUMAN	374897	609969	ENSG00000189001
+O60911	Cathepsin L2	4	NX_O60911	CATL2_HUMAN	1515	603308	ENSG00000136943
+P00558	Phosphoglycerate kinase 1	4	NX_P00558	PGK1_HUMAN	5230	300653; 311800	ENSG00000102144
+P04075	Fructose-bisphosphate aldolase A	4	NX_P04075	ALDOA_HUMAN	226	103850; 611881	ENSG00000149925
+P07384	Calpain-1 catalytic subunit	4	NX_P07384	CAN1_HUMAN	823	114220; 616907	ENSG00000014216
+P0CG05	Ig lambda-2 chain C regions	4	NA	NA	NA	NA	NA
+P18206	Vinculin	4	NX_P18206	VINC_HUMAN	7414	193065; 611407; 613255	ENSG00000035403
+P62258	14-3-3 protein epsilon	4	NX_P62258	1433E_HUMAN	7531	605066	ENSG00000108953; ENSG00000274474
+P68871	Hemoglobin subunit beta	4	NX_P68871	HBB_HUMAN	3043	140700; 141900; 603902; 603903; 611162; 613985	ENSG00000244734
+Q9C075	Keratin, type I cytoskeletal 23	4	NX_Q9C075	K1C23_HUMAN	25984	606194	ENSG00000108244; ENSG00000263309
+A8K2U0	Alpha-2-macroglobulin-like protein 1	3	NX_A8K2U0	A2ML1_HUMAN	144568	610627	ENSG00000166535
+P00738	Haptoglobin	3	NX_P00738	HPT_HUMAN	3240	140100; 614081	ENSG00000257017
+P01011	Alpha-1-antichymotrypsin	3	NX_P01011	AACT_HUMAN	12	107280	ENSG00000196136
+P02763	Alpha-1-acid glycoprotein 1	3	NX_P02763	A1AG1_HUMAN	5004	138600	ENSG00000229314
+P18510	Interleukin-1 receptor antagonist protein	3	NX_P18510	IL1RA_HUMAN	3557	147679; 612628; 612852	ENSG00000136689
+P22528	Cornifin-B	3	NX_P22528	SPR1B_HUMAN	6699	182266	ENSG00000169469
+P30740	Leukocyte elastase inhibitor	3	NX_P30740	ILEU_HUMAN	1992	130135	ENSG00000021355
+P80188	Neutrophil gelatinase-associated lipocalin	3	NX_P80188	NGAL_HUMAN	3934	600181	ENSG00000148346
+Q15828	Cystatin-M	3	NX_Q15828	CYTM_HUMAN	1474	601891	ENSG00000175315
+Q9HCY8	Protein S100-A14	3	NX_Q9HCY8	S10AE_HUMAN	57402	607986	ENSG00000189334
+P01623	Ig kappa chain V-III region	3	NA	NA	NA	NA	NA
+P01877	Ig alpha-2 chain C region	3	NX_P01877	IGHA2_HUMAN	NA	147000	ENSG00000211890
+P06396	Gelsolin	3	NX_P06396	GELS_HUMAN	2934	105120; 137350	ENSG00000148180
+P14735	Insulin-degrading enzyme	3	NX_P14735	IDE_HUMAN	3416	146680	ENSG00000119912
+P20933	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase	3	NX_P20933	ASPG_HUMAN	175	208400; 613228	ENSG00000038002
+P25788	Proteasome subunit alpha type-3	3	NX_P25788	PSA3_HUMAN	5684	176843; 176845	ENSG00000100567
+P26641	Elongation factor 1-gamma	3	NX_P26641	EF1G_HUMAN	1937	130593	ENSG00000254772
+P36952	Serpin B5	3	NX_P36952	SPB5_HUMAN	5268	154790	ENSG00000206075
+P40926	Malate dehydrogenase, mitochondrial	3	NX_P40926	MDHM_HUMAN	4191	154100; 617339	ENSG00000146701
+Q9Y6R7	IgGFc-binding protein	3	NX_Q9Y6R7	FCGBP_HUMAN	8857	617553	ENSG00000281123
+O95274	Ly6/PLAUR domain-containing protein 3	2	NX_O95274	LYPD3_HUMAN	27076	609484	ENSG00000124466
+P00491	Purine nucleoside phosphorylase	2	NX_P00491	PNPH_HUMAN	4860	164050; 613179	ENSG00000198805
+P04080	Cystatin-B	2	NX_P04080	CYTB_HUMAN	1476	254800; 601145	ENSG00000160213
+P09972	Fructose-bisphosphate aldolase C	2	NX_P09972	ALDOC_HUMAN	230	103870	ENSG00000109107
+P19012	Keratin, type I cytoskeletal 15	2	NX_P19012	K1C15_HUMAN	3866	148030	ENSG00000171346
+P20930	Filaggrin	2	NX_P20930	FILA_HUMAN	2312	135940; 146700; 605803	ENSG00000143631
+Q96FX8	p53 apoptosis effector related to PMP-22	2	NX_Q96FX8	PERP_HUMAN	64065	609301	ENSG00000112378
+Q9UIV8	Serpin B13	2	NX_Q9UIV8	SPB13_HUMAN	5275	604445	ENSG00000197641
+P01625	Ig kappa chain V-IV region Len	2	NA	NA	NA	NA	NA
+P01765	Ig heavy chain V-III region TIL	2	NA	NA	NA	NA	NA
+P01766	Ig heavy chain V-III region BRO	2	NX_P01766	HV313_HUMAN	NA	NA	ENSG00000211942; ENSG00000282286
+P01860	Ig gamma-3 chain C region	2	NX_P01860	IGHG3_HUMAN	NA	147120	NA
+P01871	Ig mu chain C region	2	NX_P01871	IGHM_HUMAN	NA	147020; 601495	ENSG00000211899; ENSG00000282657
+P05090	Apolipoprotein D	2	NX_P05090	APOD_HUMAN	347	107740	ENSG00000189058
+P06870	Kallikrein-1	2	NX_P06870	KLK1_HUMAN	3816	147910; 615953	ENSG00000167748
+P07858	Cathepsin B	2	NX_P07858	CATB_HUMAN	1508	116810	ENSG00000164733
+P08865	40S ribosomal protein SA	2	NX_P08865	RSSA_HUMAN	3921	150370; 271400	ENSG00000168028
+P11279	Lysosome-associated membrane glycoprotein 1	2	NX_P11279	LAMP1_HUMAN	3916	153330	ENSG00000185896
+P13473	Lysosome-associated membrane glycoprotein 2	2	NX_P13473	LAMP2_HUMAN	3920	300257; 309060	ENSG00000005893
+P19971	Thymidine phosphorylase	2	NX_P19971	TYPH_HUMAN	1890	131222; 603041	ENSG00000025708
+P23284	Peptidyl-prolyl cis-trans isomerase B	2	NX_P23284	PPIB_HUMAN	5479	123841; 259440	ENSG00000166794
+P23396	40S ribosomal protein S3	2	NX_P23396	RS3_HUMAN	6188	600454	ENSG00000149273
+P25705	ATP synthase subunit alpha, mitochondrial	2	NX_P25705	ATPA_HUMAN	498	164360; 615228; 616045	ENSG00000152234
+P27482	Calmodulin-like protein 3	2	NX_P27482	CALL3_HUMAN	810	114184	ENSG00000178363
+P31949	Protein S100-A11	2	NX_P31949	S10AB_HUMAN	6282	603114	ENSG00000163191
+P40121	Macrophage-capping protein	2	NX_P40121	CAPG_HUMAN	822	153615	ENSG00000042493
+P42357	Histidine ammonia-lyase	2	NX_P42357	HUTH_HUMAN	3034	235800; 609457	ENSG00000084110
+P47756	F-actin-capping protein subunit beta	2	NX_P47756	CAPZB_HUMAN	832	601572	ENSG00000077549
+P48637	Glutathione synthetase	2	NX_P48637	GSHB_HUMAN	2937	231900; 266130; 601002	ENSG00000100983
+P49720	Proteasome subunit beta type-3	2	NX_P49720	PSB3_HUMAN	5691	602176	ENSG00000277791; ENSG00000275903
+P50395	Rab GDP dissociation inhibitor beta	2	NX_P50395	GDIB_HUMAN	2665	600767	ENSG00000057608
+P59998	Actin-related protein 2/3 complex subunit 4	2	NX_P59998	ARPC4_HUMAN	10093	604226	ENSG00000241553
+P61160	Actin-related protein 2	2	NX_P61160	ARP2_HUMAN	10097	604221	ENSG00000138071
+P61916	Epididymal secretory protein E1	2	NX_P61916	NPC2_HUMAN	10577	601015; 607625	ENSG00000119655
+P04745	Alpha-amylase 1	23	NX_P04745	AMY1_HUMAN	276; 277; 278	104700; 104701; 104702	ENSG00000174876; ENSG00000187733; ENSG00000237763
+Q9NZT1	Calmodulin-like protein 5	8	NX_Q9NZT1	CALL5_HUMAN	51806	605183	ENSG00000178372
+P12273	Prolactin-inducible protein	6	NX_P12273	PIP_HUMAN	5304	176720	ENSG00000159763
+Q96DA0	Zymogen granule protein 16 homolog B	5	NX_Q96DA0	ZG16B_HUMAN	124220	NA	ENSG00000162078; ENSG00000283056
+P01036	Cystatin-S	5	NX_P01036	CYTS_HUMAN	1472	123857	ENSG00000101441
+Q8TAX7	Mucin-7	2	NX_Q8TAX7	MUC7_HUMAN	4589	158375; 600807	ENSG00000171195
+P01037	Cystatin-SN	2	NX_P01037	CYTN_HUMAN	1469	123855	ENSG00000170373
+P09228	Cystatin-SA	2	NX_P09228	CYTT_HUMAN	1470	123856	ENSG00000170369
diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/Mucilli.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mucilli.txt	Fri Feb 16 03:37:16 2018 -0500
@@ -0,0 +1,167 @@
+P04264
+P35908
+P35527
+P04259
+P13647
+P08779
+P02533
+Q04695
+P01040
+P13645
+P59665
+Q01469
+Q9NZT1
+P22531
+P04792
+P01834
+Q96KK5
+Q06830
+P60709
+P13646
+P31949
+P06702
+P14923
+Q13835
+P60174
+P07737
+P62805
+P31947
+P10599
+P15924
+Q6UWP8
+P02768
+Q6KB66
+P12035
+P47929
+P04406
+P17931
+Q3ZCW2
+P63167
+P63104
+P0CG48
+Q5XKE5
+P11142
+P06733
+Q7Z794
+P01593
+Q9NZH8
+P14174
+P01620
+P36952
+P68104
+O60814
+Q8N1N4
+P00338
+Q02413
+P07355
+P52907
+Q6ZVX7
+P08865
+P09211
+Q96P63
+P68371
+P30041
+P27482
+P08107
+P22392
+P29508
+P01861
+Q08188
+Q9C075
+P14618
+P31025
+P02679
+P54652
+Q13748
+P01857
+P80188
+P35321
+P02675
+P19013
+Q14CN4
+P37802
+P05783
+P51149
+P01876
+P28072
+Q86YZ3
+Q5T749
+P28070
+P05109
+P02671
+P58107
+Q5T750
+P04040
+P00558
+P62244
+P03973
+Q6E0U4
+P47756
+P13639
+P68431
+P32119
+Q8WVV4
+Q96QA5
+P68871
+Q9Y337
+P11021
+P01871
+P61626
+P25311
+P22735
+P30050
+P06576
+O43175
+O43790
+P37837
+P04083
+P04075
+P02545
+P50990
+O43707
+Q5D862
+P17900
+O75223
+Q14134
+Q08554
+P60842
+P00738
+P07476
+P05120
+P28074
+O15523
+P25787
+P13489
+P05091
+P31944
+P23490
+P05090
+P06396
+P49862
+P18206
+P15880
+P05089
+P40925
+P40926
+P20933
+Q9UIV8
+Q5VVQ6
+P07900
+P02788
+Q9Y3R4
+P23526
+P07339
+Q15517
+Q8IW75
+P49189
+P01023
+P26641
+P61978
+P10809
+P29401
+O75369
+Q15365
+P29373
+P14735
+Q14210
+Q9Y277
diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/RPKM.txt
--- a/test-data/RPKM.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,417 +0,0 @@
-G000005
-G000008
-G000009
-G000012
-G000028
-G000029
-G000030
-G000061
-G000101
-G000147
-G000165
-G000177
-G000185
-G000195
-G000237
-G000259
-G000262
-G000302
-G000305
-G000306
-G000311
-G000316
-G000355
-G000356
-G000370
-G000376
-G000377
-G000381
-G000412
-G000418
-G000420
-G000426
-G000447
-G000490
-G000514
-G000517
-G000547
-G000581
-G000665
-G000696
-G000701
-G000704
-G000705
-G000711
-G000714
-G000715
-G000717
-G000720
-G000721
-G000722
-G000725
-G000726
-G000728
-G000749
-G000783
-G000824
-G000851
-G000857
-G000899
-G000902
-G000934
-G000951
-G000962
-G000966
-G000984
-G000985
-G000987
-G001006
-G001007
-G001029
-G001043
-G001045
-G001051
-G001053
-G001061
-G001093
-G001102
-G001105
-G001107
-G001112
-G001115
-G001123
-G001136
-G001171
-G001189
-G001218
-G001226
-G001247
-G001283
-G001287
-G001288
-G001317
-G001319
-G001328
-G001343
-G001351
-G001352
-G001359
-G001360
-G001362
-G001386
-G001409
-G001431
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/TC.txt
--- a/test-data/TC.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,548 +0,0 @@
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/TMM.txt
--- a/test-data/TMM.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1190 +0,0 @@
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/UQ.txt
--- a/test-data/UQ.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1213 +0,0 @@
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diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/Venn_diagram_html.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Venn_diagram_html.html	Fri Feb 16 03:37:16 2018 -0500
@@ -0,0 +1,228 @@
+<!DOCTYPE html>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<html>
+	<head>
+		<title>Jvenn+</title>
+		<meta charset="UTF-8">
+		<meta name="version" content="2.0.1">
+		<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>
+		<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>
+		<style type="text/css">
+			#js-alert {
+				width: 90%;
+				margin-right: auto;
+				margin-left: auto;
+			}
+			#content {
+				width: 90%;
+				margin-right: auto;
+				margin-left: auto;
+			}
+			.clear {
+				clear: both;
+				height: 0px;
+				width: 100%;
+				float: none !important;
+			}
+			ul.nav-tabs {
+				margin-bottom: 30px;
+			}
+			#venn-filters {
+				padding: 10px;
+				background-color: #FFF;
+				background-clip: padding-box;
+				border: 1px solid rgba(0, 0, 0, 0.15);
+				border-radius: 4px;
+				box-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);
+				margin-right: auto;
+				margin-left: auto;
+				margin-bottom: 30px;
+			}
+			#byFilters-jvenn {
+				margin-right: auto;
+				margin-left: auto;
+			}
+			#venn-filters ul {
+				list-style-type: none;
+			}
+		</style>
+
+		<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
+		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
+		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
+		<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>
+		<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
+		<script type="text/javascript">
+			/***************************************************************
+			*  Copyright notice
+			*
+			*  (c) 2014 PF bioinformatique de Toulouse
+			*  All rights reserved
+			* 
+			*
+			*  This script is an adaptation of the venny script developed by
+			*  Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:
+			*  Oliveros, J.C. (2007) VENNY. An interactive tool for comparing 
+			*  lists with Venn Diagrams.
+			*  http://bioinfogp.cnb.csic.es/tools/venny/index.html.
+			*  It is distributed under the terms of the GNU General Public 
+			*  License as published by the Free Software Foundation; either 
+			*  version 2 of the License, or (at your option) any later version.
+			*
+			*  The GNU General Public License can be found at
+			*  http://www.gnu.org/copyleft/gpl.html.
+			*
+			*  This script is distributed in the hope that it will be useful,
+			*  but WITHOUT ANY WARRANTY; without even the implied warranty of
+			*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+			*  GNU General Public License for more details.
+			*
+			*  This copyright notice MUST APPEAR in all copies of the script!
+			***************************************************************/
+			!function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\{"+l[e]+"\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for an undefined object");t="ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz",e="";do for(e="",l=0;12>l;l++)e+=t[Math.floor(Math.random()*t.length)];while(s[e]);return e}function e(s,t){var e,l,r,o={};for(s=s.split(","),t=t||10,e=0;e<s.length;e+=2)l="&"+s[e+1]+";",r=parseInt(s[e],t),o[l]="&#"+r+";";return o["\\xa0"]="&#160;",o}function l(s){var t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[s]||t.start}function r(s){var t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[s]||t.alphabetic}var 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+		</script>
+		<script type="text/javascript">
+			/*
+			 * HTMLTable.js 0.1.0 - HTMLTable Library
+			 *
+			 * Copyright (c) 2015 Escudie Frederic
+			 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
+			 */
+			function HTMLtable(e){var t,r,n=e,a=";";this.deleteColumns=function(e){for(var a=n.getElementsByTagName("tr"),o=0;o<a.length;o++){s=0;var i=a[o].getElementsByTagName("td");0==i.length&&(i=a[o].getElementsByTagName("th"));for(var v=0,s=0;s<t[1];s++)if(!r[o][s]){var f=i[v].getAttribute("colspan");if(null!=f)for(var m=0;f>m;m++){if(in_array(s+m,e)){var u=i[v].getAttribute("colspan");u-1==0?i[v].removeAttribute("colspan"):i[v].setAttribute("colspan",u-1)}if(null==i[v].getAttribute("colspan")){var h=i[v];a[o].removeChild(h),v--}}else if(in_array(s,e)){var h=i[v];a[o].removeChild(h),v--}v++}}l(),g()},this.filter=function(e,a){var l=new RegExp(e),g=new Array;null!=a&&a||(g.c0=!0);for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)r[i][f]||(l.test(v[s].innerHTML)&&(g["c"+f]=!0),s++)}for(var m=new Array,u=0;u<t[1];u++)void 0===g["c"+u]&&m.push(u);this.deleteColumns(m)},this.getModel=function(){return n};var l=function(){for(var e=0,r=0,a=n.getElementsByTagName("tr"),l=0;l<a.length;l++){var g=0;e++;var o=a[l].getElementsByTagName("td");0==o.length&&(o=a[l].getElementsByTagName("th"));for(var i=0;i<o.length;i++){var v=o[i].getAttribute("colspan");g+=null==v?1:parseInt(v)}g>r&&(r=g)}t=new Array(2),t[0]=e,t[1]=r},g=function(){r=new Array(t[0]);for(var e=0;e<t[0];e++){r[e]=new Array(t[1]);for(var a=0;a<t[1];a++)r[e][a]=!1}for(var l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){v=0;var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)if(!r[g][v]){var s=0,f=0,m=o[i].getAttribute("rowspan");null!=m&&(s=parseInt(m)-1);var u=o[i].getAttribute("colspan");null!=u&&(f=parseInt(u)-1);for(var h=s;h>=0;h--)for(var y=f;y>=0;y--)(0!=h||0!=y)&&(r[g+h][v+y]=!0);i++}}};this.replace=function(e,a,l){var g=new RegExp(e);null==a&&(a=""),null==l&&(l="");for(var o=n.getElementsByTagName("tr"),i=0;i<o.length;i++){f=0;var v=o[i].getElementsByTagName("td");if(0!=v.length)for(var s=0,f=0;f<t[1];f++)if(!r[i][f]){var m=g.exec(v[s].innerHTML);null!=m&&(void 0===m[1]&&(m[1]=""),v[s].innerHTML=a+m[1]+l),s++}}},this.toCSV=function(){for(var e="",l=n.getElementsByTagName("tr"),g=0;g<l.length;g++){var o=l[g].getElementsByTagName("td");0==o.length&&(o=l[g].getElementsByTagName("th"));for(var i=0,v=0;v<t[1];v++)r[g][v]||(e+=o[i].innerHTML,i++),e+=a;e=e.substr(0,e.length-1)+"\n"}return e},l(),g()}var in_array=function(e,t){for(var r in t)if(t[r]==e)return!0;return!1};
+			
+			/*
+			 * dataTableExtractor.plugin.js 0.1.0 - datatableExport Library
+			 *
+			 * Copyright (c) 2015 Escudie Frederic
+			 * Licensed under the MIT (http://www.opensource.org/licenses/mit-license.php) license.
+			 */
+			!function(t){t.fn.datatableExport=function(a){var e={anchor_id:t(this).attr("id"),table_id:null,csv_separator:";",omitted_columns:[]},n=t.extend(e,a);if(!t(this).length)throw"The element where the datatableExport is called does not exist.";if(void 0==n.anchor_id)throw"The datatableExport plugin must be called on an element with id.";if(null==n.table_id)throw"You must set the table_id parameter in datatableExport plugin.";if(!t("#"+n.table_id))throw"The datatable '#"+n.table_id+"' cannot be retieve in DOM.";return this.each(function(){var a=t(this);a.on("click",function(){t.fn.datatableExport.csv(n.anchor_id,n.table_id,n.csv_separator,n.omitted_columns)})})},t.fn.datatableExport.cleanCellMarkup=function(a,e){t.parseHTML(e);t("#"+a).append('<div class="hidden data-tmp">'+e+"</div>"),t("#"+a+" .data-tmp").find("input").each(function(){var a="";a=t(this).is(":checkbox")?t(this).is(":checked")?"true":"false":t(this).val(),t(this).replaceWith(a)});var n=t("#"+a+" .data-tmp").text();return t("#"+a+" .data-tmp").remove(),n},t.fn.datatableExport.csv=function(a,e,n,i){var l="",r=t("#"+e).DataTable(),d=t("#"+e+" thead")[0],o=new HTMLtable(d.cloneNode(!0));o.deleteColumns(i),l+=o.toCSV();var c=r.rows().data();t.each(c,function(e,n){for(var r="",d=0;d<n.length;d++)-1==t.inArray(d,i)&&(r+='"'+t.fn.datatableExport.cleanCellMarkup(a,n[d])+'";');""!=r&&(r=r.slice(0,-1)),l+=r+"\n"}),t("#"+a+"-extract-csv").length||t("#"+a).append('<a id="'+a+'-extract-csv" href="data:text/csv;charset=UTF-8,'+encodeURI(l)+'" download="data.csv" style="display:none;"></a>'),t("#"+a+"-extract-csv")[0].click()}}(jQuery);
+		</script>		
+		
+		<script type="text/javascript">
+/*
+$(document).ready(function(){
+  $('#example').jvenn({
+    series: [{
+    	name: {A: 'Actors',
+               B: 'Singers'},
+    	data: {A: ["Arnold Schwarzenegger", "Jack Nicholson", "Robert de Niro", "Harrison Ford"], B: ["Freddy Mercury", "Ricky Martin", "Celine Dion"], AB: ["Marilyn Monroe", "Barbra Streisand", "Dean Martin"]},
+    	values: {A: 4, B: 3, AB: 3}
+    }],
+  });
+});
+*/
+var jvenn_data = {"series": [{"values": {"A": 59, "C": 71, "B": 80, "BC": 9, "AC": 14, "ABC": 27, "AB": 51}, "data": {"A": ["P0DMV9", "Q9Y6R7", "P30740", "P68363", "O75635", "O60911", "P61160", "Q15828", "P23284", "P20930", "P01860", "Q96FX8", "P62937", "Q15149", "P25705", "P19971", "O75342", "Q92820", "P25788", "Q9HCY8", "P19012", "Q8TAX7", "P42357", "P50395", "P01766", "P40121", "P04080", "Q9HC84", "P59998", "P23396", "P00491", "P62258", "P01623", "P31151", "Q6P4A8", "P63261", "P01877", "P09228", "P48637", "P07858", "P07384", "P06870", "Q9UI42", "P35579", "P13473", "P62987", "P04745", "P49720", "P11279", "P18510", "Q14574", "P02538", "P48594", "A8K2U0", "P09972", "O95274", "P01037", "P0CG05", "P00441"], "C": ["P04217", "P02649", "Q7Z351", "P08758", "Q9UBC9", "P02760", "O95436", "P02647", "P15814", "Q9NSK0", "P01717", "P04117", "Q13885", "P01591", "O95613", "P01880", "P04233", "P01598", "P01621", "Q9UL77", "P05362", "P01024", "Q86SJ6", "P12429", "P43652", "P22897", "P06313", "B4E1Z4", "P01008", "A2IPI6", "P02790", "P61769", "P00450", "Q08380", "P02751", "Q8NF17", "Q14624", "P0C0L5", "P0C0L4", "Q9UL83", "P08238", "P02766", "Q9UL86", "P02774", "P05155", "P11686", "P01622", "Q6N093", "P04637", "Q96S96", "P62807", "P23528", "P10909", "A4F255", "P00734", "P19827", "Q16378", "P01714", "P11217", "A0A0U1RVJ5", "P01617", "P01611", "P04196", "P01613", "P02747", "P80748", "A0N5G5", "Q8IWL2", "Q9BYE4", "P06681", "Q6MZX7"], "B": ["Q7Z794", "P51149", "P17900", "Q96KK5", "P10809", "O43175", "Q6ZVX7", "P01861", "P14174", "P01593", "Q15365", "P37802", "P29373", "P30050", "Q6E0U4", "P23526", "Q13748", "P05120", "Q14134", "P68431", "P35527", "Q5XKE5", "O15523", "P25787", "P22392", "P49189", "P61978", "P32119", "Q5VVQ6", "Q8IW75", "P01620", "P02671", "P62244", "P0CG48", "P02675", "Q9Y277", "P02679", "P02533", "Q9Y337", "P12035", "P52907", "P35321", "P13489", "P29401", "P04264", "Q14210", "P28074", "P40925", "P28070", "P28072", "Q14CN4", "Q9Y3R4", "P13647", "P54652", "Q08554", "P08107", "P30041", "P06702", "O43790", "Q96QA5", "P23490", "P22735", "P13645", "P17931", "Q3ZCW2", "P68104", "P06576", "Q5T749", "P05091", "O60814", "P37837", "P22531", "P03973", "P63167", "P05783", "P50990", "P15880", "P35908", "P07476", "P49862"], "BC": ["Q13835", "P01023", "P59665", "Q15517", "P05109", "P60709", "P62805", "Q5D862", "P07737"], "AC": ["P02787", "P01833", "P01625", "P22528", "Q9UGM3", "Q96DA0", "P02763", "P61916", "P01009", "P12273", "Q13867", "P01765", "P01036", "P01011"], "ABC": ["P02768", "P10599", "P07355", "Q01469", "P68871", "P07900", "P15924", "P25311", "Q86YZ3", "P05089", "Q08188", "P04406", "P07339", "P06396", "P00338", "P61626", "P04083", "Q02413", "P27482", "P01871", "P80188", "P31947", "P31025", "Q96P63", "P63104", "P00738", "P02788"], "AB": ["P08779", "P04259", "O75223", "P47756", "P06733", "P20933", "Q9NZH8", "P09211", "P04792", "P36952", "P01040", "P60174", "P26641", "P14618", "P31944", "Q8N1N4", "P04075", "P14923", "Q8WVV4", "O75369", "P00558", "P19013", "Q5T750", "P14735", "P47929", "Q06830", "P29508", "P68371", "Q9NZT1", "P11142", "P40926", "P01876", "P58107", "P01834", "P18206", "Q04695", "P08865", "P13646", "P02545", "P04040", "P13639", "P05090", "Q6KB66", "P01857", "Q6UWP8", "Q9UIV8", "Q9C075", "O43707", "P11021", "P31949", "P60842"]}, "name": {"A": "Lacombe", "C": "Bredberg", "B": "Mucilli"}}], "displaySwitch": "true", "shortNumber": "true", "displayStat": "true"} ;
+$(document).ready(function(){
+  $('#example').jvenn(jvenn_data);
+});
+
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//
+			// Data
+			//
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//var processed_filters = ###PORCESSED_FILTERS### ;
+			/* Example:
+				['filterA', 'filterB', 'filterC']
+			*/
+			//var global_results = ###GLOBAL_RESULTS### ; 
+			/* Example: 
+				{
+					'nb_clstr_kept': 100,
+					'nb_clstr_ini': 300,
+					'nb_seq_kept': 100,
+					'nb_seq_ini': 100000
+				}
+			*/
+			//var by_samples_results = ###SAMPLES_RESULTS### ;
+			/* Example:
+				{
+					'sampleA':{
+						'filtered':{
+							'filterA': 10,
+							'filterB': 20
+						},
+						'initial': 75,
+						'kept': 50
+					},
+					'sampleB':{
+						'filtered':{
+							'filterB': 20,
+						},
+						'initial': 110,
+						'kept': 90
+					}
+				}
+			*/
+			//var by_filters_results = ###FILTERS_RESULTS### ;
+			/* Example:
+				[
+					{'filters':['filterA'], 'count': 10},
+					{'filters':['filterB'], 'count': 20},
+					{'filters':['filterC'], 'count': 30},
+					{'filters':['filterA', 'filterB'], 'count': 1},
+					{'filters':['filterA', 'filterC'], 'count': 2},
+					{'filters':['filterB', 'filterC'], 'count': 3},
+					{'filters':['filterA', 'filterB', 'filterC'], 'count': 4}
+				];
+			*/
+			
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			//
+			// Main
+			//
+			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
+			$(function() {
+				// Remove alert
+				$('#js-alert').remove();
+				$('#content').removeClass("hidden");
+				
+				// Load active tab
+				global_filters_load();
+				intersections_filters_load();
+				
+				// Add tab listener
+				$('.nav-tabs a').click(function (e) {
+					e.preventDefault();
+					$(this).tab('show');
+					if( $(this).attr('href') == "#view-by-samples" && $('#view-by-samples').hasClass('disabled') ){
+						$('#view-by-samples').removeClass('disabled')
+						samples_filters_load( "filter-log" );
+					}
+				})
+			});
+		</script>
+
+	</head>
+	<body>
+		<!-- Alert -->
+		<p id="js-alert" class="alert alert-warning">
+                javascript is needed to display data.<br />
+                If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
+		</p>
+		
+        <!-- Content -->
+	<div id="example"></div>
+        </div>
+
+		
+	</body>
+</html>
diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/Venn_text_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Venn_text_output.txt	Fri Feb 16 03:37:16 2018 -0500
@@ -0,0 +1,81 @@
+Lacombe	Bredberg	Mucilli	Mucilli_Bredberg	Lacombe_Bredberg	Lacombe_Mucilli_Bredberg	Lacombe_Mucilli	
+P0DMV9	P04217	Q7Z794	Q13835	P02787	P02768	P08779	
+Q9Y6R7	P02649	P51149	P01023	P01833	P10599	P04259	
+P30740	Q7Z351	P17900	P59665	P01625	P07355	O75223	
+P68363	P08758	Q96KK5	Q15517	P22528	Q01469	P47756	
+O75635	Q9UBC9	P10809	P05109	Q9UGM3	P68871	P06733	
+O60911	P02760	O43175	P60709	Q96DA0	P07900	P20933	
+P61160	O95436	Q6ZVX7	P62805	P02763	P15924	Q9NZH8	
+Q15828	P02647	P01861	Q5D862	P61916	P25311	P09211	
+P23284	P15814	P14174	P07737	P01009	Q86YZ3	P04792	
+P20930	Q9NSK0	P01593		P12273	P05089	P36952	
+P01860	P01717	Q15365		Q13867	Q08188	P01040	
+Q96FX8	P04117	P37802		P01765	P04406	P60174	
+P62937	Q13885	P29373		P01036	P07339	P26641	
+Q15149	P01591	P30050		P01011	P06396	P14618	
+P25705	O95613	Q6E0U4			P00338	P31944	
+P19971	P01880	P23526			P61626	Q8N1N4	
+O75342	P04233	Q13748			P04083	P04075	
+Q92820	P01598	P05120			Q02413	P14923	
+P25788	P01621	Q14134			P27482	Q8WVV4	
+Q9HCY8	Q9UL77	P68431			P01871	O75369	
+P19012	P05362	P35527			P80188	P00558	
+Q8TAX7	P01024	Q5XKE5			P31947	P19013	
+P42357	Q86SJ6	O15523			P31025	Q5T750	
+P50395	P12429	P25787			Q96P63	P14735	
+P01766	P43652	P22392			P63104	P47929	
+P40121	P22897	P49189			P00738	Q06830	
+P04080	P06313	P61978			P02788	P29508	
+Q9HC84	B4E1Z4	P32119				P68371	
+P59998	P01008	Q5VVQ6				Q9NZT1	
+P23396	A2IPI6	Q8IW75				P11142	
+P00491	P02790	P01620				P40926	
+P62258	P61769	P02671				P01876	
+P01623	P00450	P62244				P58107	
+P31151	Q08380	P0CG48				P01834	
+Q6P4A8	P02751	P02675				P18206	
+P63261	Q8NF17	Q9Y277				Q04695	
+P01877	Q14624	P02679				P08865	
+P09228	P0C0L5	P02533				P13646	
+P48637	P0C0L4	Q9Y337				P02545	
+P07858	Q9UL83	P12035				P04040	
+P07384	P08238	P52907				P13639	
+P06870	P02766	P35321				P05090	
+Q9UI42	Q9UL86	P13489				Q6KB66	
+P35579	P02774	P29401				P01857	
+P13473	P05155	P04264				Q6UWP8	
+P62987	P11686	Q14210				Q9UIV8	
+P04745	P01622	P28074				Q9C075	
+P49720	Q6N093	P40925				O43707	
+P11279	P04637	P28070				P11021	
+P18510	Q96S96	P28072				P31949	
+Q14574	P62807	Q14CN4				P60842	
+P02538	P23528	Q9Y3R4					
+P48594	P10909	P13647					
+A8K2U0	A4F255	P54652					
+P09972	P00734	Q08554					
+O95274	P19827	P08107					
+P01037	Q16378	P30041					
+P0CG05	P01714	P06702					
+P00441	P11217	O43790					
+	A0A0U1RVJ5	Q96QA5					
+	P01617	P23490					
+	P01611	P22735					
+	P04196	P13645					
+	P01613	P17931					
+	P02747	Q3ZCW2					
+	P80748	P68104					
+	A0N5G5	P06576					
+	Q8IWL2	Q5T749					
+	Q9BYE4	P05091					
+	P06681	O60814					
+	Q6MZX7	P37837					
+		P22531					
+		P03973					
+		P63167					
+		P05783					
+		P50990					
+		P15880					
+		P35908					
+		P07476					
+		P49862					
\ No newline at end of file
diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/venn_diagram_summary.html
--- a/test-data/venn_diagram_summary.html	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,228 +0,0 @@
-<!DOCTYPE html>
-<!--
-# Copyright (C) 2015 INRA
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
--->
-<html>
-	<head>
-		<title>Jvenn+</title>
-		<meta charset="UTF-8">
-		<meta name="version" content="2.0.1">
-		<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>
-		<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>
-		<style type="text/css">
-			#js-alert {
-				width: 90%;
-				margin-right: auto;
-				margin-left: auto;
-			}
-			#content {
-				width: 90%;
-				margin-right: auto;
-				margin-left: auto;
-			}
-			.clear {
-				clear: both;
-				height: 0px;
-				width: 100%;
-				float: none !important;
-			}
-			ul.nav-tabs {
-				margin-bottom: 30px;
-			}
-			#venn-filters {
-				padding: 10px;
-				background-color: #FFF;
-				background-clip: padding-box;
-				border: 1px solid rgba(0, 0, 0, 0.15);
-				border-radius: 4px;
-				box-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176);
-				margin-right: auto;
-				margin-left: auto;
-				margin-bottom: 30px;
-			}
-			#byFilters-jvenn {
-				margin-right: auto;
-				margin-left: auto;
-			}
-			#venn-filters ul {
-				list-style-type: none;
-			}
-		</style>
-
-		<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>
-		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>
-		<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>
-		<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>
-		<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
-		<script type="text/javascript">
-			/***************************************************************
-			*  Copyright notice
-			*
-			*  (c) 2014 PF bioinformatique de Toulouse
-			*  All rights reserved
-			* 
-			*
-			*  This script is an adaptation of the venny script developed by
-			*  Juan Carlos Oliveros, BioinfoGP, CNB-CSIC:
-			*  Oliveros, J.C. (2007) VENNY. An interactive tool for comparing 
-			*  lists with Venn Diagrams.
-			*  http://bioinfogp.cnb.csic.es/tools/venny/index.html.
-			*  It is distributed under the terms of the GNU General Public 
-			*  License as published by the Free Software Foundation; either 
-			*  version 2 of the License, or (at your option) any later version.
-			*
-			*  The GNU General Public License can be found at
-			*  http://www.gnu.org/copyleft/gpl.html.
-			*
-			*  This script is distributed in the hope that it will be useful,
-			*  but WITHOUT ANY WARRANTY; without even the implied warranty of
-			*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-			*  GNU General Public License for more details.
-			*
-			*  This copyright notice MUST APPEAR in all copies of the script!
-			***************************************************************/
-			!function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\{"+l[e]+"\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for an undefined object");t="ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz",e="";do for(e="",l=0;12>l;l++)e+=t[Math.floor(Math.random()*t.length)];while(s[e]);return e}function e(s,t){var e,l,r,o={};for(s=s.split(","),t=t||10,e=0;e<s.length;e+=2)l="&"+s[e+1]+";",r=parseInt(s[e],t),o[l]="&#"+r+";";return o["\\xa0"]="&#160;",o}function l(s){var t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[s]||t.start}function r(s){var t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[s]||t.alphabetic}var 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"G001333", "G002056", "G003746", "G001026", "G001219", "G000431", "G000167", "G001609", "G002206", "G004445", "G002750", "G003340", "G001629", "G004350", "G002901", "G002187", "G002510", "G002040"], "ABEF": ["G001344", "G004551", "G001597", "G000748", "G000620", "G000628", "G000629", "G001296", "G003031", "G001726", "G002038", "G002032", "G001687", "G002526", "G001465", "G004491", "G004144", "G001665", "G001668", "G004467", "G002650", "G004462", "G000845", "G004547", "G002146", "G002624", "G002625", "G002620", "G004648", "G004860", "G000362", "G004643", "G004795", "G004334", "G003661", "G000218", "G003143", "G003928", "G001169", "G000273", "G003110", "G001893", "G001895", "G001897", "G004814", "G002085", "G002245", "G002246", "G002242", "G002715", "G005148", "G005149", "G000444", "G005142", "G004729", "G004082", "G002882", "G002881", "G000788", "G001306", "G000668", "G000540", "G001090", "G000646", "G003446", "G001393", "G004885", "G002402", "G002401", "G000231", "G000144", "G001001", "G002913", "G005033", "G001949", "G002814", "G001944", "G002816", "G001766", "G001940", "G002760", "G001542", "G002585", "G001232", "G002589", "G001628", "G003695", "G001626", "G002007", "G004421", "G002061", "G003043", "G002107", "G003044", "G002104", "G004191", "G003915", "G001434", "G001433", "G004699", "G004698", "G004695", "G004697", "G003183", "G002613", "G002612", "G004458", "G004104", "G004850", "G004593", "G002436", "G005274", "G002200", "G003980", "G003823", "G002209", "G001997", "G001991", "G000982", "G004604", "G003139", "G003138", "G000323", "G004982", "G000116", "G005002", "G005001", "G003522", "G001146", "G001906", "G002446", "G002444", "G000022", "G000023", "G000027", "G000181", "G000180", "G005178", "G000186", "G001278", "G001279", "G001374", "G001379", "G001271", "G004108", "G000759", "G000612", "G005091", "G003411", "G000754", "G002535", "G004972", "G002380", "G002929", "G001972", "G001878", "G001970", "G001877", "G001697", "G001694", "G001978", "G001474", "G004481", "G001478", "G004484", "G004485", "G003381", "G001579", "G004999", "G000976", "G000879", "G004411", "G004410", "G000872", "G003099", "G002655", "G002654", "G004328", "G000274", "G004325", "G004635", "G000270", "G004439", "G003179", "G003953", "G003776", "G003898", "G003956", "G003770", "G003892", "G000203", "G003670", "G004520", "G004745", "G004743", "G004740", "G001155", "G005121", "G004021", "G005231", "G004730", "G005234", "G002996", "G005237", "G000475", "G003818", "G002879", "G002878", "G001707", "G000790", "G004867", "G000497", "G005196", "G005199", "G000498", "G002470", "G001836", "G001385", "G001015", "G002774", "G001937", "G001201", "G002599", "G000834", "G003057", "G002694", "G003588", "G002973", "G002970", "G002979", "G003906", "G003903", "G000988", "G000909", "G002183", "G003637", "G004568", "G000904", "G003733", "G002609", "G003227", "G002184", "G004704", "G003836", "G000232", "G000338", "G000339", "G003643", "G004203", "G000238", "G003649", "G003648", "G004014", "G000041", "G004011", "G001802", "G000194", "G002734", "G003199", "G002301", "G002303", "G000427", "G001119", "G000584", "G001116", "G001110", "G001854", "G002942", "G002941", "G003784", "G004944", "G004947", "G003013", "G003542", "G001809", "G001960", "G001746", "G001749", "G002838", "G001968", "G002391", "G001645", "G001644", "G001646", "G000944", "G003306", "G003302", "G004404", "G004892", "G003261", "G003308", "G001244", "G001241", "G003286", "G000268", "G003282", "G003281", "G004237", "G000261", "G005172", "G005173", "G003160", "G001121", "G004123", "G000404", "G003766", "G004120", "G004539", "G004243", "G003601", "G000890", "G000896", "G000894", "G005118", "G004059", "G000002", "G005114", "G000411", "G002348", "G005073", "G002344", "G004832", "G002341", "G000098", "G003116", "G000301", "G004332", "G004331", "G005204", "G000466", "G005200", "G002868", "G002865", "G002860", "G002863", "G003500", "G003503", "G002194", "G002714", "G005182", "G000526", "G000524", "G004883", "G002464", "G002469", "G002749", "G001929", "G005220", "G004088", "G001022", "G001604", "G001355", "G001606", "G001353", "G001210", "G004302", "G000637", "G000635", "G000631", "G000737", "G000827", "G000730", "G002120", "G003025", "G003342", "G002687", "G001289", "G001324", "G001325", "G001281", "G003938", "G004022", "G003931", "G003163", "G001517", "G001457", "G002051", "G003233", "G003791", "G003238", "G003480", "G003337", "G004470", "G004610", "G000358", "G003800", "G004657", "G004874", "G003808", "G000352", "G004625", "G002228", "G001711", "G004784", "G004377", "G004007", "G001179", "G000078", "G000660", "G004392", "G002096", "G004398", "G002093", "G005227", "G002705", "G002251", "G001108", "G000592", "G001756", "G000772", "G001825", "G002891", "G002439", "G002489", "G002484", "G002957", "G003474", "G002388", "G001083", "G001080", "G002555", "G001394", "G002843", "G001952", "G001073", "G001810", "G001812", "G001776", "G002414", "G002417", "G001227", "G001495", "G001559", "G000468", "G000810", "G000709", "G002671", "G003375", "G004435", "G003076", "G003296", "G000253", "G004220", "G000254", "G001424", "G003949", "G002458", "G000929", "G000927", "G001578", "G004137", "G004501", "G003612", "G004245", "G003201", "G003972", "G004989", "G004988", "G004755", "G004040", "G000405", "G005265", "G004044", "G004980", "G004829", "G002213", "G004290", "G003850", "G004346", "G000317", "G001049", "G003701", "G003538", "G000530", "G000534", "G004535", "G002757", "G002459", "G001910", "G002751", "G002758", "G002320", "G000031", "G001032"], "BDEF": ["G004118"], "A": ["G001905", "G000130", "G000349", "G002946", "G004042", "G002598", "G002420", "G002190", "G004395", "G000389", "G001410", "G000053", "G000189", "G001293", "G001291", "G003379", "G002906", "G000222", "G003407", "G003764", "G002974", "G003644", "G002782", "G002172", "G002079", "G003965", "G000773", "G004036", "G001047", "G004140", "G004711", "G000880", "G004716", "G003934", "G003416", "G004838", "G002205", "G002365", "G004085", "G003453", "G003681", "G001788", "G002084", "G001421", "G003174", "G003630", "G002752", "G004453", "G003690", "G004978", "G002192", "G003433", "G003739", "G003598", "G004208", "G003498", "G001071", "G002640", "G004526", "G000200", "G003425", "G003490", "G002287"], "ACEF": [], "C": [], "B": ["G004580", "G001204", "G002864", "G002803", "G003997", "G001436", "G005184", "G003688", "G000569", "G003544", "G001298", "G004121", "G005031", "G001761", "G004037", "G005014", "G001485", "G004679", "G000570", "G000881", "G001563", "G003758", "G001696", "G004115"], "E": [], "D": [], "ABF": ["G000655", "G004703", "G000046"], "F": ["G003283", "G002316", "G000950", "G001094", "G000919", "G003033", "G003401", "G003940", "G003662", "G002781", "G003484", "G001580", "G002176", "G004364", "G005211", "G005018", "G004659", "G004637", "G001481", "G002220", "G000718", "G000731", "G003851", "G001387", "G002455", "G001139", "G003155"], "ABCDE": [], "EF": ["G001936", "G004930", "G004238", "G000875", "G001275", "G002311", "G003088", "G001657", "G003943", "G001072", "G001509", "G002635", "G000309", "G000471", "G004081"], "ABD": [], "CF": [], "CE": [], "CD": [], "ADF": [], "ADE": [], "ABDE": [], "ACDF": [], "BDF": [], "ABDF": [], "ACDEF": ["G005180"], "ABCDEF": ["G001598", "G000305", "G001343", "G000749", "G005089", "G004967", "G003403", "G001725", "G001729", "G001467", "G001461", "G005250", "G000962", "G000966", "G004096", "G001507", "G004466", "G004543", "G004469", "G003080", "G002628", "G002626", "G003322", "G004649", "G004793", "G004260", "G003142", "G003881", "G004034", "G002899", "G005131", "G000061", "G001890", "G001891", "G002361", "G001899", "G002369", "G002368", "G003041", "G002710", "G002711", "G005222", "G000447", "G002969", "G002968", "G002885", "G000783", "G002967", "G000547", "G001093", "G000665", "G004887", "G002569", "G001820", "G004922", "G004925", "G000147", "G001007", "G001751", "G001760", "G001765", "G001547", "G000714", "G000715", "G000717", "G001780", "G000711", "G001623", "G001620", "G004428", "G003366", "G004907", "G003593", "G003592", "G002101", "G003594", "G004192", "G003919", "G004210", "G003912", "G001539", "G001431", "G003589", "G000934", "G003628", "G002616", "G002610", "G003962", "G003747", "G003964", "G004856", "G004671", "G004992", "G005276", "G004772", "G005273", "G002202", "G003828", "G001998", "G001995", "G001993", "G004351", "G004353", "G000985", "G000984", "G000987", "G002416", "G001283", "G001226", "G001051", "G001053", "G002722", "G001904", "G002331", "G002332", "G002333", "G001123", "G005176", "G005175", "G000028", "G000029", "G000185", "G005094", "G005095", "G002533", "G003558", "G003550", "G001753", "G001976", "G001975", "G002385", "G002384", "G002024", "G001791", "G003388", "G004487", "G004468", "G001575", "G004558", "G001218", "G003093", "G002658", "G002153", "G003315", "G003317", "G004329", "G000420", "G004324", "G001409", "G003177", "G004258", "G000012", "G005126", "G002373", "G000381", "G000376", "G000377", "G004735", "G001704", "G001703", "G003511", "G005192", "G000490", "G005198", "G002475", "G004932", "G004934", "G005043", "G002779", "G002594", "G002595", "G000721", "G000720", "G000725", "G000726", "G001630", "G000728", "G002981", "G001633", "G001288", "G002693", "G002691", "G003059", "G002050", "G002053", "G002975", "G002055", "G002054", "G001840", "G003905", "G003901", "G004161", "G004160", "G001328", "G003634", "G000902", "G003229", "G004119", "G002601", "G004113", "G003222", "G005248", "G005241", "G005243", "G001983", "G002231", "G001987", "G003645", "G000237", "G003125", "G005019", "G000514", "G001061", "G001189", "G000165", "G000696", "G002309", "G000195", "G001386", "G000426", "G004064", "G001115", "G005169", "G000581", "G000517", "G001112", "G002497", "G001362", "G001360", "G003464", "G002011", "G003619", "G003543", "G002833", "G002784", "G002834", "G001748", "G001640", "G001560", "G001565", "G003304", "G003305", "G003865", "G002648", "G004578", "G001247", "G002641", "G004589", "G004623", "G000262", "G001649", "G000899", "G005266", "G003948", "G004241", "G004532", "G000008", "G000009", "G000418", "G000412", "G002928", "G002267", "G003843", "G003847", "G002346", "G000302", "G003113", "G000306", "G004330", "G005201", "G005203", "G005202", "G001736", "G003502", "G005188", "G002199", "G005185", "G005055", "G002297", "G000356", "G001926", "G001605", "G001352", "G001351", "G001359", "G002998", "G002992", "G003023", "G002682", "G002902", "G002048", "G002044", "G001287", "G004170", "G003230", "G004577", "G000857", "G000851", "G004479", "G003486", "G004471", "G002972", "G004475", "G004477", "G004718", "G004307", "G000355", "G004712", "G004713", "G004714", "G004715", "G004783", "G004273", "G004373", "G003154", "G004004", "G005024", "G001171", "G000177", "G001880", "G001889", "G002709", "G002254", "G002383", "G002702", "G005254", "G005255", "G005159", "G004099", "G001102", "G005154", "G004095", "G001107", "G001105", "G002894", "G001319", "G002896", "G002488", "G001317", "G002953", "G003902", "G003579", "G002551", "G004895", "G002001", "G001951", "G001819", "G002797", "G001771", "G001772", "G001554", "G000705", "G000704", "G000701", "G000951", "G001650", "G001651", "G002077", "G003075", "G001006", "G000259", "G004187", "G004565", "G004131", "G004136", "G003208", "G003611", "G005119", "G004762", "G005269", "G005268", "G004768", "G005264", "G005263", "G004299", "G002097", "G000311", "G000316", "G004612", "G005212", "G004349", "G004618", "G001136", "G000101", "G001045", "G001043", "G000005", "G003539", "G003220", "G002755", "G002453", "G005105", "G000030", "G002282"], "ABCDF": [], "BCEF": [], "CDE": [], "CDF": [], "CDEF": ["G004293", "G005246"], "ABE": ["G002821", "G004455", "G003971", "G000024", "G004855"], "ABCD": [], "ABCEF": ["G004239", "G003173", "G004545", "G004051", "G002566", "G002518", "G001525", "G000722", "G001029", "G004391", "G000370", "G003082", "G003602", "G002180", "G005167", "G004789", "G000824", "G005259"], "BDE": [], "ACDE": []}, "name": {"A": "DESeq", "C": "RPKM", "B": "FQ", "E": "TMM", "D": "TC", "F": "UQ"}}], "displaySwitch": "true", "shortNumber": "true", "displayStat": "true"} ;
-$(document).ready(function(){
-  $('#example').jvenn(jvenn_data);
-});
-
-			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-			//
-			// Data
-			//
-			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-			//var processed_filters = ###PORCESSED_FILTERS### ;
-			/* Example:
-				['filterA', 'filterB', 'filterC']
-			*/
-			//var global_results = ###GLOBAL_RESULTS### ; 
-			/* Example: 
-				{
-					'nb_clstr_kept': 100,
-					'nb_clstr_ini': 300,
-					'nb_seq_kept': 100,
-					'nb_seq_ini': 100000
-				}
-			*/
-			//var by_samples_results = ###SAMPLES_RESULTS### ;
-			/* Example:
-				{
-					'sampleA':{
-						'filtered':{
-							'filterA': 10,
-							'filterB': 20
-						},
-						'initial': 75,
-						'kept': 50
-					},
-					'sampleB':{
-						'filtered':{
-							'filterB': 20,
-						},
-						'initial': 110,
-						'kept': 90
-					}
-				}
-			*/
-			//var by_filters_results = ###FILTERS_RESULTS### ;
-			/* Example:
-				[
-					{'filters':['filterA'], 'count': 10},
-					{'filters':['filterB'], 'count': 20},
-					{'filters':['filterC'], 'count': 30},
-					{'filters':['filterA', 'filterB'], 'count': 1},
-					{'filters':['filterA', 'filterC'], 'count': 2},
-					{'filters':['filterB', 'filterC'], 'count': 3},
-					{'filters':['filterA', 'filterB', 'filterC'], 'count': 4}
-				];
-			*/
-			
-			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-			//
-			// Main
-			//
-			///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-			$(function() {
-				// Remove alert
-				$('#js-alert').remove();
-				$('#content').removeClass("hidden");
-				
-				// Load active tab
-				global_filters_load();
-				intersections_filters_load();
-				
-				// Add tab listener
-				$('.nav-tabs a').click(function (e) {
-					e.preventDefault();
-					$(this).tab('show');
-					if( $(this).attr('href') == "#view-by-samples" && $('#view-by-samples').hasClass('disabled') ){
-						$('#view-by-samples').removeClass('disabled')
-						samples_filters_load( "filter-log" );
-					}
-				})
-			});
-		</script>
-
-	</head>
-	<body>
-		<!-- Alert -->
-		<p id="js-alert" class="alert alert-warning">
-                javascript is needed to display data.<br />
-                If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.
-		</p>
-		
-        <!-- Content -->
-	<div id="example"></div>
-        </div>
-
-		
-	</body>
-</html>
diff -r 9d4f20618ab4 -r 760470ddb9ca test-data/venn_diagram_text_output.txt
--- a/test-data/venn_diagram_text_output.txt	Sun Nov 26 19:09:40 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,485 +0,0 @@
-FQ_UQ	FQ_RPKM_TC	DESeq_FQ_RPKM_TMM_UQ	DESeq_FQ_TMM_UQ	FQ	DESeq_TMM_UQ	UQ	FQ_RPKM_TC_TMM_UQ	DESeq_TC_TMM_UQ	DESeq_FQ_TC_TMM_UQ	DESeq	DESeq_FQ	DESeq_TMM	DESeq_FQ_TMM	DESeq_FQ_UQ	DESeq_UQ	FQ_TMM_UQ	TMM_UQ	DESeq_RPKM_TC_TMM_UQ	DESeq_FQ_RPKM_TC_TMM_UQ	RPKM_TC_TMM_UQ	FQ_TC_TMM_UQ	
-G004321	G002462	G004239	G001344	G004580	G001195	G003283	G005214	G001285	G001197	G001905	G002826	G000080	G002821	G000655	G001203	G002976	G001936	G005180	G001598	G004293	G004118	
-G002493		G003173	G004551	G001204	G000114	G002316		G002062	G001193	G000130	G004420	G004384	G004455	G004703	G004708	G000483	G004930		G000305	G005246		
-G001369		G004545	G001597	G002864	G004177	G000950			G001052	G000349	G003424	G002405	G003971	G000046	G003149		G004238		G001343			
-G004173		G004051	G000748	G002803	G001510	G001094			G003936	G002946	G000164	G003427	G000024		G002637		G000875		G000749			
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-			G002251																			
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\ No newline at end of file
diff -r 9d4f20618ab4 -r 760470ddb9ca venn_diagram.xml
--- a/venn_diagram.xml	Sun Nov 26 19:09:40 2017 -0500
+++ b/venn_diagram.xml	Fri Feb 16 03:37:16 2018 -0500
@@ -22,7 +22,6 @@
                     <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
                         <option value="list">Copy/paste your identifiers </option>
                         <option value="file">Input file containing your identifiers</option>
-                        
                     </param>
                     <when value="file">
                         <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" />
@@ -54,61 +53,33 @@
 	    <test>
 	        <repeat name="series">
 	            <conditional name="se">
-	                <param name="input" value="mq_file" />
-	                <param name="mq_file" value="DESeq.txt" />
-	                <param name="header" value="false" />
+	                <param name="input" value="file" />
+	                <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" />
+	                <param name="header" value="true" />
 	                <param name="ncol" value="c1" />
-	                <param name="name" value="DESeq" />
-	            </conditional>
-	        </repeat>
-	        <repeat name="series">
-	            <conditional name="se">
-	                <param name="input" value="mq_file" />
-	                <param name="mq_file" value="FQ.txt" />
-	                <param name="header" value="false" />
-	                <param name="ncol" value="c1" />
-	                <param name="name" value="FQ" />
-	            </conditional>
-	        </repeat>
-	        <repeat name="series">
-	            <conditional name="se">
-	                <param name="input" value="mq_file" />
-	                <param name="mq_file" value="RPKM.txt" />
-	                <param name="header" value="false" />
-	                <param name="ncol" value="c1" />
-	                <param name="name" value="RPKM" />
+	                <param name="name" value="Lacombe" />
 	            </conditional>
 	        </repeat>
 	        <repeat name="series">
 	            <conditional name="se">
-	                <param name="input" value="mq_file" />
-	                <param name="mq_file" value="TC.txt" />
+	                <param name="input" value="file" />
+	                <param name="file" value="Mucilli.txt" />
 	                <param name="header" value="false" />
 	                <param name="ncol" value="c1" />
-	                <param name="name" value="TC" />
+	                <param name="name" value="Mucilli" />
 	            </conditional>
 	        </repeat>
 	        <repeat name="series">
 	            <conditional name="se">
-	                <param name="input" value="mq_file" />
-	                <param name="mq_file" value="TMM.txt" />
+	                <param name="input" value="file" />
+	                <param name="file" value="Bredberg.txt" />
 	                <param name="header" value="false" />
 	                <param name="ncol" value="c1" />
-	                <param name="name" value="TMM" />
+	                <param name="name" value="Bredberg" />
 	            </conditional>
 	        </repeat>
-	        <repeat name="series">
-	            <conditional name="se">
-	                <param name="input" value="mq_file" />
-	                <param name="mq_file" value="UQ.txt" />
-	                <param name="header" value="false" />
-	                <param name="ncol" value="c1" />
-	                <param name="name" value="UQ" />
-	            </conditional>
-	        </repeat>
-	        <output name="output_summary" file="venn_diagram_summary.html" />
-	        <output name="output_text" file="venn_diagram_text_output.txt" />
-	                
+	        <output name="output_summary" file="Venn_diagram_html.html" />
+	        <output name="output_text" file="Venn_text_output.txt" />      
 	    </test>
 	</tests>
 	<help>
@@ -120,21 +91,22 @@
 * **Query file:** A file containing different information of proteins, could be output of previous components.
 
 * **File of a list of IDs:** .TXT format, each line contains 1 ID
-    
-    AMY1A
-    
- 	ALB
- 	
- 	IGKC
- 	
- 	CSTA
- 	
- 	IGHA1
- 	
- 	ACTG1
+
+  AMY1A
+
+  ALB	
+
+  IGKC	
+
+  CSTA	
+
+  IGHA1 	
+
+  ACTG1
 
 * **List of IDs:** IDs separated by a space
-    AMY1A ALB IGKC CSTA IGHA1 ACTG1
+
+  AMY1A ALB IGKC CSTA IGHA1 ACTG1
 
 If you choose a file, it is necessary to specify the column where you would like to perform the comparison.