changeset 5:88c1fd2ac110 draft default tip

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents d4e9f7546dfa
children
files data/block_Y.tsv data/meta_sample.tsv data/metadata_mirna.tsv data/metadata_mrna.tsv data/metadata_protein.tsv data/mirna.tsv data/mrna.tsv data/param_integration_mixOmics.txt data/protein.tsv data/response_var.tsv data/var_interest.tsv macros_mixomics.xml macros_viscorvar.xml mixomics_blocksplsda.R mixomics_blocksplsda.xml mixomics_plotindiv.xml mixomics_plotvar.xml viscorvar_circlecor.xml viscorvar_computematsimilarity.xml viscorvar_matcoraddvar.xml viscorvar_networkvar.R viscorvar_networkvar.xml
diffstat 22 files changed, 1426 insertions(+), 118 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/block_Y.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,151 @@
+	Basal	Her2	LumA
+A0FJ	1	0	0
+A13E	1	0	0
+A0G0	1	0	0
+A0SX	1	0	0
+A143	1	0	0
+A0DA	1	0	0
+A0B3	1	0	0
+A0I2	1	0	0
+A0RT	1	0	0
+A131	1	0	0
+A124	1	0	0
+A1B6	1	0	0
+A1AZ	1	0	0
+A0YM	1	0	0
+A04P	1	0	0
+A04T	1	0	0
+A0AT	1	0	0
+A0AL	1	0	0
+A0CE	1	0	0
+A07R	1	0	0
+A0FL	1	0	0
+A150	1	0	0
+A0E0	1	0	0
+A0U4	1	0	0
+A0XU	1	0	0
+A0AV	1	0	0
+A0AR	1	0	0
+A0RX	1	0	0
+A0D2	1	0	0
+A0CM	1	0	0
+A0WX	1	0	0
+A0T0	1	0	0
+A0T2	1	0	0
+A04U	1	0	0
+A0JL	1	0	0
+A147	1	0	0
+A0B9	1	0	0
+A1AI	1	0	0
+A14X	1	0	0
+A12V	1	0	0
+A1AY	1	0	0
+A0D0	1	0	0
+A0SK	1	0	0
+A128	1	0	0
+A04D	1	0	0
+A0A7	0	1	0
+A094	0	1	0
+A12L	0	1	0
+A0I9	0	1	0
+A0EE	0	1	0
+A135	0	1	0
+A152	0	1	0
+A18P	0	1	0
+A18R	0	1	0
+A08X	0	1	0
+A0TX	0	1	0
+A09X	0	1	0
+A1AT	0	1	0
+A12Q	0	1	0
+A12T	0	1	0
+A0RH	0	1	0
+A07I	0	1	0
+A04W	0	1	0
+A12P	0	1	0
+A0EQ	0	1	0
+A0D1	0	1	0
+A09G	0	1	0
+A1B0	0	1	0
+A14P	0	1	0
+A0T1	0	1	0
+A137	0	1	0
+A13Z	0	1	0
+A08L	0	1	0
+A0IK	0	1	0
+A12D	0	1	0
+A0XN	0	0	1
+A0B0	0	0	1
+A18S	0	0	1
+A0CS	0	0	1
+A0EI	0	0	1
+A0IO	0	0	1
+A0T6	0	0	1
+A1AU	0	0	1
+A07Z	0	0	1
+A0XS	0	0	1
+A1BD	0	0	1
+A08T	0	0	1
+A12Y	0	0	1
+A0J5	0	0	1
+A18F	0	0	1
+A0AS	0	0	1
+A0DV	0	0	1
+A140	0	0	1
+A0SU	0	0	1
+A12A	0	0	1
+A0RM	0	0	1
+A0AZ	0	0	1
+A0EW	0	0	1
+A0XW	0	0	1
+A12B	0	0	1
+A0BP	0	0	1
+A0RG	0	0	1
+A0T7	0	0	1
+A08A	0	0	1
+A0DK	0	0	1
+A0SH	0	0	1
+A18N	0	0	1
+A06P	0	0	1
+A15L	0	0	1
+A0YL	0	0	1
+A1AL	0	0	1
+A133	0	0	1
+A086	0	0	1
+A0I8	0	0	1
+A0EA	0	0	1
+A09A	0	0	1
+A0DS	0	0	1
+A1B1	0	0	1
+A0X0	0	0	1
+A1AP	0	0	1
+A0W5	0	0	1
+A0JF	0	0	1
+A1AV	0	0	1
+A0RO	0	0	1
+A08Z	0	0	1
+A0RV	0	0	1
+A0DP	0	0	1
+A0EX	0	0	1
+A15R	0	0	1
+A0FD	0	0	1
+A0ES	0	0	1
+A0BM	0	0	1
+A0EU	0	0	1
+A12X	0	0	1
+A146	0	0	1
+A0CD	0	0	1
+A0BQ	0	0	1
+A04A	0	0	1
+A0CT	0	0	1
+A0TZ	0	0	1
+A03L	0	0	1
+A1AK	0	0	1
+A0E1	0	0	1
+A0H7	0	0	1
+A0FS	0	0	1
+A0BS	0	0	1
+A08O	0	0	1
+A12H	0	0	1
+A15E	0	0	1
+A0W4	0	0	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/meta_sample.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,151 @@
+	Y
+A0FJ	Basal
+A13E	Basal
+A0G0	Basal
+A0SX	Basal
+A143	Basal
+A0DA	Basal
+A0B3	Basal
+A0I2	Basal
+A0RT	Basal
+A131	Basal
+A124	Basal
+A1B6	Basal
+A1AZ	Basal
+A0YM	Basal
+A04P	Basal
+A04T	Basal
+A0AT	Basal
+A0AL	Basal
+A0CE	Basal
+A07R	Basal
+A0FL	Basal
+A150	Basal
+A0E0	Basal
+A0U4	Basal
+A0XU	Basal
+A0AV	Basal
+A0AR	Basal
+A0RX	Basal
+A0D2	Basal
+A0CM	Basal
+A0WX	Basal
+A0T0	Basal
+A0T2	Basal
+A04U	Basal
+A0JL	Basal
+A147	Basal
+A0B9	Basal
+A1AI	Basal
+A14X	Basal
+A12V	Basal
+A1AY	Basal
+A0D0	Basal
+A0SK	Basal
+A128	Basal
+A04D	Basal
+A0A7	Her2
+A094	Her2
+A12L	Her2
+A0I9	Her2
+A0EE	Her2
+A135	Her2
+A152	Her2
+A18P	Her2
+A18R	Her2
+A08X	Her2
+A0TX	Her2
+A09X	Her2
+A1AT	Her2
+A12Q	Her2
+A12T	Her2
+A0RH	Her2
+A07I	Her2
+A04W	Her2
+A12P	Her2
+A0EQ	Her2
+A0D1	Her2
+A09G	Her2
+A1B0	Her2
+A14P	Her2
+A0T1	Her2
+A137	Her2
+A13Z	Her2
+A08L	Her2
+A0IK	Her2
+A12D	Her2
+A0XN	LumA
+A0B0	LumA
+A18S	LumA
+A0CS	LumA
+A0EI	LumA
+A0IO	LumA
+A0T6	LumA
+A1AU	LumA
+A07Z	LumA
+A0XS	LumA
+A1BD	LumA
+A08T	LumA
+A12Y	LumA
+A0J5	LumA
+A18F	LumA
+A0AS	LumA
+A0DV	LumA
+A140	LumA
+A0SU	LumA
+A12A	LumA
+A0RM	LumA
+A0AZ	LumA
+A0EW	LumA
+A0XW	LumA
+A12B	LumA
+A0BP	LumA
+A0RG	LumA
+A0T7	LumA
+A08A	LumA
+A0DK	LumA
+A0SH	LumA
+A18N	LumA
+A06P	LumA
+A15L	LumA
+A0YL	LumA
+A1AL	LumA
+A133	LumA
+A086	LumA
+A0I8	LumA
+A0EA	LumA
+A09A	LumA
+A0DS	LumA
+A1B1	LumA
+A0X0	LumA
+A1AP	LumA
+A0W5	LumA
+A0JF	LumA
+A1AV	LumA
+A0RO	LumA
+A08Z	LumA
+A0RV	LumA
+A0DP	LumA
+A0EX	LumA
+A15R	LumA
+A0FD	LumA
+A0ES	LumA
+A0BM	LumA
+A0EU	LumA
+A12X	LumA
+A146	LumA
+A0CD	LumA
+A0BQ	LumA
+A04A	LumA
+A0CT	LumA
+A0TZ	LumA
+A03L	LumA
+A1AK	LumA
+A0E1	LumA
+A0H7	LumA
+A0FS	LumA
+A0BS	LumA
+A08O	LumA
+A12H	LumA
+A15E	LumA
+A0W4	LumA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/metadata_mirna.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,185 @@
+Variable	metadata_var1	metadata_var2	metadata_var3
+hsa-let-7a-1	182	79	44
+hsa-let-7a-2	137	151	74
+hsa-let-7a-3	53	136	136
+hsa-let-7b	32	168	147
+hsa-let-7c	169	33	78
+hsa-let-7d	114	21	160
+hsa-let-7e	43	4	22
+hsa-let-7f-1	58	152	67
+hsa-let-7f-2	128	148	85
+hsa-let-7g	30	70	69
+hsa-let-7i	141	90	125
+hsa-mir-100	118	45	6
+hsa-mir-101-1	13	57	165
+hsa-mir-101-2	34	38	176
+hsa-mir-103-1	183	23	138
+hsa-mir-103-2	105	142	54
+hsa-mir-106a	150	51	58
+hsa-mir-106b	9	94	37
+hsa-mir-107	39	66	168
+hsa-mir-10a	173	122	79
+hsa-mir-10b	135	87	96
+hsa-mir-125a	107	117	10
+hsa-mir-125b-1	22	140	42
+hsa-mir-126	87	83	104
+hsa-mir-127	140	35	33
+hsa-mir-128-1	104	62	49
+hsa-mir-128-2	18	183	150
+hsa-mir-1287	84	49	68
+hsa-mir-1301	47	14	173
+hsa-mir-1307	152	120	52
+hsa-mir-130a	171	126	31
+hsa-mir-130b	2	113	64
+hsa-mir-132	181	44	157
+hsa-mir-134	78	170	134
+hsa-mir-139	90	81	117
+hsa-mir-140	149	16	9
+hsa-mir-141	127	143	124
+hsa-mir-142	67	89	180
+hsa-mir-143	25	77	115
+hsa-mir-144	161	131	162
+hsa-mir-145	88	95	100
+hsa-mir-146a	79	160	83
+hsa-mir-146b	126	133	21
+hsa-mir-148a	155	86	172
+hsa-mir-148b	24	177	155
+hsa-mir-149	177	153	93
+hsa-mir-150	21	121	95
+hsa-mir-151	6	132	41
+hsa-mir-152	89	149	179
+hsa-mir-155	35	141	169
+hsa-mir-15a	71	93	99
+hsa-mir-15b	180	124	146
+hsa-mir-16-1	131	43	3
+hsa-mir-16-2	10	156	63
+hsa-mir-17	166	13	40
+hsa-mir-181a-1	85	169	129
+hsa-mir-181a-2	44	61	182
+hsa-mir-181b-1	73	182	32
+hsa-mir-181c	157	80	183
+hsa-mir-181d	49	67	159
+hsa-mir-182	76	129	61
+hsa-mir-183	178	139	56
+hsa-mir-185	167	114	65
+hsa-mir-186	146	109	62
+hsa-mir-191	40	40	181
+hsa-mir-192	125	63	16
+hsa-mir-193a	109	172	94
+hsa-mir-193b	17	96	116
+hsa-mir-194-1	162	32	102
+hsa-mir-194-2	176	99	122
+hsa-mir-195	86	157	119
+hsa-mir-196a-1	119	30	97
+hsa-mir-196b	3	104	88
+hsa-mir-197	83	58	178
+hsa-mir-199a-1	12	123	82
+hsa-mir-199a-2	158	52	142
+hsa-mir-199b	145	173	2
+hsa-mir-19b-2	168	17	77
+hsa-mir-200a	69	54	127
+hsa-mir-200b	14	39	53
+hsa-mir-200c	70	84	143
+hsa-mir-203	136	130	7
+hsa-mir-205	142	73	76
+hsa-mir-20a	100	36	98
+hsa-mir-21	94	176	51
+hsa-mir-210	27	102	109
+hsa-mir-214	110	105	174
+hsa-mir-218-2	91	27	50
+hsa-mir-22	160	98	91
+hsa-mir-221	138	69	151
+hsa-mir-222	116	92	73
+hsa-mir-223	16	137	43
+hsa-mir-2355	20	100	152
+hsa-mir-23a	54	3	11
+hsa-mir-23b	72	178	158
+hsa-mir-24-1	45	85	34
+hsa-mir-24-2	147	134	105
+hsa-mir-25	123	25	133
+hsa-mir-26a-2	64	101	30
+hsa-mir-26b	7	107	118
+hsa-mir-27a	101	150	17
+hsa-mir-27b	46	180	60
+hsa-mir-28	112	15	167
+hsa-mir-29a	36	64	1
+hsa-mir-29b-1	59	22	19
+hsa-mir-29b-2	74	179	101
+hsa-mir-29c	98	106	144
+hsa-mir-3065	134	159	46
+hsa-mir-3074	93	46	166
+hsa-mir-30a	143	181	114
+hsa-mir-30b	38	147	156
+hsa-mir-30c-2	1	76	111
+hsa-mir-30d	42	47	84
+hsa-mir-30e	172	71	57
+hsa-mir-32	15	55	48
+hsa-mir-320a	57	5	170
+hsa-mir-324	33	184	175
+hsa-mir-328	144	37	29
+hsa-mir-330	56	115	8
+hsa-mir-331	95	8	18
+hsa-mir-337	108	108	149
+hsa-mir-338	97	19	163
+hsa-mir-339	175	175	66
+hsa-mir-340	99	2	72
+hsa-mir-342	120	12	123
+hsa-mir-345	164	48	71
+hsa-mir-34a	81	145	70
+hsa-mir-3607	174	24	135
+hsa-mir-361	63	125	137
+hsa-mir-3613	68	34	154
+hsa-mir-3647	111	111	161
+hsa-mir-365-1	92	72	4
+hsa-mir-365-2	52	146	139
+hsa-mir-3653	102	118	80
+hsa-mir-374a	26	166	27
+hsa-mir-374b	37	6	14
+hsa-mir-375	31	127	20
+hsa-mir-378	29	56	103
+hsa-mir-379	55	154	140
+hsa-mir-381	139	112	132
+hsa-mir-409	5	116	55
+hsa-mir-423	65	161	15
+hsa-mir-424	122	164	36
+hsa-mir-425	66	165	145
+hsa-mir-429	41	138	87
+hsa-mir-451	129	88	112
+hsa-mir-452	117	59	184
+hsa-mir-454	62	60	106
+hsa-mir-455	106	7	121
+hsa-mir-484	133	53	126
+hsa-mir-486	170	171	75
+hsa-mir-497	61	155	38
+hsa-mir-500a	130	31	59
+hsa-mir-501	179	163	81
+hsa-mir-505	159	162	26
+hsa-mir-532	50	11	110
+hsa-mir-539	165	74	107
+hsa-mir-542	51	135	24
+hsa-mir-574	4	174	25
+hsa-mir-576	8	103	120
+hsa-mir-582	184	65	47
+hsa-mir-584	60	10	141
+hsa-mir-589	132	28	130
+hsa-mir-590	163	26	153
+hsa-mir-625	82	110	5
+hsa-mir-628	154	42	35
+hsa-mir-629	153	29	113
+hsa-mir-660	75	18	86
+hsa-mir-664	103	119	28
+hsa-mir-7-1	96	9	108
+hsa-mir-708	28	97	23
+hsa-mir-744	23	20	177
+hsa-mir-769	115	158	148
+hsa-mir-874	124	91	90
+hsa-mir-9-1	11	144	89
+hsa-mir-9-2	19	41	39
+hsa-mir-92a-1	80	78	45
+hsa-mir-92a-2	121	75	12
+hsa-mir-92b	113	128	164
+hsa-mir-93	77	1	171
+hsa-mir-96	48	68	92
+hsa-mir-98	156	50	131
+hsa-mir-99a	151	167	13
+hsa-mir-99b	148	82	128
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/metadata_mrna.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,201 @@
+Variable	metadata_var1	metadata_var2	metadata_var3
+RTN2	67	127	139
+NDRG2	18	110	40
+CCDC113	117	72	99
+FAM63A	77	190	113
+ACADS	94	80	186
+GMDS	149	14	178
+HLA-H	140	21	168
+SEMA4A	80	124	126
+ETS2	107	178	11
+LIMD2	35	68	71
+NME3	85	45	92
+ZEB1	188	139	63
+CDCP1	198	13	169
+GIYD2	84	2	97
+RTKN2	180	168	54
+MANSC1	153	99	32
+TAGLN	152	93	195
+IFIT3	108	196	101
+ARL4C	66	151	112
+HTRA1	157	121	125
+KIF13B	130	3	110
+CPPED1	113	97	167
+SKAP2	150	30	114
+ASPM	128	108	34
+KDM4B	40	157	145
+TBXAS1	55	39	127
+MT1X	189	5	21
+MED13L	135	173	157
+SNORA8	71	174	182
+RGS1	28	200	161
+CBX6	133	96	84
+WWC2	184	152	67
+TNFRSF12A	169	140	53
+ZNF552	21	164	42
+MAPRE2	193	23	131
+SEMA5A	109	106	83
+STAT5A	174	182	64
+FLI1	43	60	116
+COL15A1	127	134	93
+C7orf55	74	177	85
+ASF1B	45	114	78
+FUT8	38	141	98
+LASS4	60	16	100
+SQLE	115	166	138
+GPC4	53	65	88
+AKAP12	196	90	152
+AGL	69	95	61
+ADAMTS4	156	57	29
+EPHB3	90	183	189
+MAP3K1	23	123	107
+PRNP	70	181	4
+PROM2	111	59	190
+SLCO3A1	175	150	46
+SNHG1	47	191	187
+PRKCDBP	119	180	103
+MXI1	32	70	102
+CSF1R	110	103	143
+TANC2	129	78	24
+SLC19A2	7	9	177
+RHOU	36	128	95
+C4orf34	75	40	165
+LRIG1	39	149	133
+DOCK8	167	18	65
+BOC	98	67	25
+C11orf52	100	34	86
+S100A16	116	44	183
+NRARP	179	87	81
+TTC23	14	189	69
+TBC1D4	103	63	119
+DEPDC6	3	81	59
+ILDR1	9	85	111
+SDC1	143	98	106
+STC2	64	86	197
+DTWD2	166	47	159
+TCF4	105	69	38
+ITPR2	65	154	129
+DPYD	82	112	141
+NME1	178	109	41
+EGLN3	102	135	68
+CD302	120	105	58
+AHR	41	58	77
+LAPTM4B	126	83	188
+OCLN	185	144	149
+HIST1H2BK	139	61	37
+HDAC11	57	15	57
+C18orf1	132	148	27
+C6orf192	89	53	50
+AMPD3	29	38	122
+COL6A1	68	94	6
+RAB3IL1	146	24	22
+APBB1IP	10	8	135
+PSIP1	1	74	163
+EIF2AK2	144	33	171
+CSRP2	104	35	62
+EIF4EBP3	138	119	180
+LYN	172	120	153
+WDR76	87	175	51
+SAMD9L	34	115	150
+ASPH	173	130	176
+RBL1	134	101	105
+SLC43A3	8	158	28
+HN1	123	84	200
+TTC39A	114	50	146
+MTL5	42	54	74
+NES	124	22	90
+APOD	187	37	192
+RIN3	177	143	3
+ALCAM	15	12	140
+C1orf38	25	170	158
+PLCD3	197	28	26
+BSPRY	11	41	47
+NTN4	2	165	55
+IL1R1	192	75	147
+EMP3	81	167	70
+ZKSCAN1	162	169	166
+FMNL2	54	142	162
+OGFRL1	194	153	173
+IRF5	19	25	87
+IGSF3	168	145	118
+DBP	44	160	104
+CNN2	181	10	94
+CAMK2D	195	185	196
+SIGIRR	163	64	185
+AKAP9	155	29	79
+ICA1	101	126	91
+FGD5	141	104	155
+DSG2	4	199	132
+E2F1	6	195	80
+QSOX1	142	27	179
+TOB1	160	198	128
+CSF3R	176	192	44
+SHROOM3	161	36	72
+CCDC80	165	32	20
+FRMD6	12	136	31
+CXCL12	79	197	18
+CCNA2	16	176	144
+TIGD5	20	71	193
+ALDH6A1	24	162	73
+POSTN	86	4	198
+FZD4	17	43	174
+NCAPG2	171	62	39
+SDC4	106	76	136
+SNED1	5	49	10
+PLEKHA4	93	6	175
+KCNAB2	78	117	19
+SH3KBP1	76	51	12
+IGSF9	159	194	17
+DNLZ	151	11	82
+S1PR3	186	100	36
+PTPRE	63	161	134
+FLJ23867	46	19	30
+PLSCR1	125	66	109
+LMO4	131	111	14
+IFITM2	48	125	120
+LRRC25	121	52	164
+TST	72	133	160
+NCF4	97	118	181
+NCOA7	51	156	89
+IL4R	200	122	148
+CCDC64B	154	42	56
+SGPP1	13	46	172
+RUNX3	122	48	123
+SLC5A6	199	56	121
+IFIH1	164	107	191
+PREX1	27	91	15
+PLAUR	95	179	124
+CDK18	136	163	170
+SLC43A2	148	20	108
+GK	96	186	1
+ICAM2	145	132	13
+YPEL2	191	146	151
+CBR1	37	82	199
+MEX3A	183	17	115
+ZNRF3	147	26	184
+PTPRM	30	88	194
+C1orf162	137	171	7
+GAS6	58	89	33
+C1QB	59	129	35
+PVRL4	26	7	117
+CTSK	88	184	137
+MRVI1	83	159	8
+LEF1	91	172	52
+PLCD4	52	102	130
+ZNF37B	49	55	16
+MEGF9	33	113	43
+GINS2	170	79	142
+FAM13A	92	31	23
+CPT1A	182	193	5
+SNX10	31	187	60
+TRIM45	158	188	48
+ELP2	61	116	2
+ALOX5	112	138	66
+AMN1	73	92	49
+CERCAM	22	1	156
+SEMA3C	56	77	96
+KRT8	99	147	76
+TP53INP2	62	131	75
+JAM3	118	137	9
+ZNF680	190	155	45
+PBX1	50	73	154
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/metadata_protein.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,143 @@
+Variable	metadata_var1	metadata_var2	metadata_var3
+14-3-3_epsilon	99	58	121
+4E-BP1	66	91	11
+4E-BP1_pS65	112	4	123
+4E-BP1_pT37	119	93	53
+4E-BP1_pT70	127	85	83
+53BP1	76	70	77
+A-Raf_pS299	134	104	69
+ACC1	22	32	78
+ACC_pS79	59	72	14
+AMPK_alpha	142	27	47
+AMPK_pT172	4	8	138
+ANLN	113	63	59
+AR	138	79	124
+ARID1A	7	6	57
+ASNS	42	15	106
+ATM	135	50	24
+Akt	35	140	4
+Akt_pS473	120	42	30
+Akt_pT308	23	20	42
+Annexin_I	14	122	140
+B-Raf	118	87	109
+Bak	11	54	117
+Bax	20	130	75
+Bcl-2	79	2	27
+Bcl-xL	124	16	21
+Beclin	39	83	112
+Bid	86	113	136
+Bim	54	31	37
+C-Raf	98	129	139
+C-Raf_pS338	65	137	41
+CD31	94	88	16
+CD49b	41	103	1
+CDK1	133	40	86
+Caspase-7_cleavedD198	52	107	74
+Caveolin-1	53	46	3
+Chk1	88	51	40
+Chk1_pS345	63	77	36
+Chk2	61	71	107
+Chk2_pT68	110	33	58
+Claudin-7	12	62	33
+Collagen_VI	78	97	94
+Cyclin_B1	89	56	93
+Cyclin_D1	96	123	17
+Cyclin_E1	111	78	82
+DJ-1	123	94	98
+Dvl3	58	116	38
+E-Cadherin	45	10	26
+EGFR	57	121	22
+EGFR_pY1068	31	76	71
+EGFR_pY1173	139	68	18
+ER-alpha	8	111	29
+ER-alpha_pS118	141	18	44
+ERK2	47	90	66
+FOXO3a	9	49	128
+Fibronectin	104	99	20
+GAB2	130	55	119
+GATA3	10	37	115
+GSK3-alpha-beta	136	12	88
+GSK3-alpha-beta_pS21_S9	131	13	51
+HER2	74	119	105
+HER2_pY1248	85	65	118
+HER3	132	48	129
+HER3_pY1289	29	26	110
+HSP70	137	75	7
+IGFBP2	122	73	15
+INPP4B	38	23	46
+IRS1	43	34	81
+JNK2	26	118	104
+JNK_pT183_pT185	93	115	68
+K-Ras	103	139	70
+Ku80	95	39	61
+LBK1	77	66	50
+Lck	64	38	134
+MAPK_pT202_Y204	82	95	91
+MEK1	34	112	142
+MEK1_pS217_S221	102	127	64
+MIG-6	69	25	87
+Mre11	116	132	116
+N-Cadherin	25	101	56
+NF-kB-p65_pS536	17	74	10
+NF2	37	120	97
+Notch1	16	64	80
+P-Cadherin	5	45	31
+PAI-1	128	24	72
+PCNA	62	9	25
+PDCD4	81	134	52
+PDK1_pS241	107	81	48
+PI3K-p110-alpha	21	86	19
+PKC-alpha	72	114	125
+PKC-alpha_pS657	70	14	54
+PKC-delta_pS664	15	47	100
+PR	50	60	35
+PRAS40_pT246	101	125	132
+PRDX1	36	96	76
+PTEN	115	53	127
+Paxillin	55	100	133
+Pea-15	83	135	9
+RBM3	1	30	23
+Rad50	108	17	113
+Rb_pS807_S811	129	11	62
+S6	13	19	43
+S6_pS235_S236	91	52	135
+S6_pS240_S244	46	44	65
+SCD1	80	141	96
+STAT3_pY705	44	1	84
+STAT5-alpha	100	67	6
+Shc_pY317	114	84	126
+Smad1	126	59	90
+Smad3	51	109	8
+Smad4	30	80	92
+Src	18	5	131
+Src_pY416	60	28	63
+Src_pY527	109	89	13
+Stathmin	19	22	45
+Syk	67	98	39
+Transglutaminase	28	142	95
+Tuberin	105	41	12
+VEGFR2	48	61	99
+XBP1	56	29	28
+XRCC1	87	108	85
+YAP_pS127	3	138	122
+YB-1	27	82	2
+YB-1_pS102	24	124	5
+alpha-Catenin	73	7	32
+beta-Catenin	68	92	55
+c-Kit	2	131	60
+c-Met_pY1235	140	105	34
+c-Myc	40	133	79
+eEF2	49	110	141
+eEF2K	71	3	49
+eIF4E	92	21	67
+mTOR	125	69	102
+mTOR_pS2448	33	102	120
+p27	6	43	111
+p27_pT157	97	117	130
+p27_pT198	90	106	108
+p38_MAPK	32	126	137
+p38_pT180_Y182	84	128	103
+p53	106	36	101
+p70S6K	121	35	114
+p70S6K_pT389	75	57	89
+p90RSK_pT359_S363	117	136	73
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/mirna.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,185 @@
+	A0FJ	A13E	A0G0	A0SX	A143	A0DA	A0B3	A0I2	A0RT	A131	A124	A1B6	A1AZ	A0YM	A04P	A04T	A0AT	A0AL	A0CE	A07R	A0FL	A150	A0E0	A0U4	A0XU	A0AV	A0AR	A0RX	A0D2	A0CM	A0WX	A0T0	A0T2	A04U	A0JL	A147	A0B9	A1AI	A14X	A12V	A1AY	A0D0	A0SK	A128	A04D	A0A7	A094	A12L	A0I9	A0EE	A135	A152	A18P	A18R	A08X	A0TX	A09X	A1AT	A12Q	A12T	A0RH	A07I	A04W	A12P	A0EQ	A0D1	A09G	A1B0	A14P	A0T1	A137	A13Z	A08L	A0IK	A12D	A0XN	A0B0	A18S	A0CS	A0EI	A0IO	A0T6	A1AU	A07Z	A0XS	A1BD	A08T	A12Y	A0J5	A18F	A0AS	A0DV	A140	A0SU	A12A	A0RM	A0AZ	A0EW	A0XW	A12B	A0BP	A0RG	A0T7	A08A	A0DK	A0SH	A18N	A06P	A15L	A0YL	A1AL	A133	A086	A0I8	A0EA	A09A	A0DS	A1B1	A0X0	A1AP	A0W5	A0JF	A1AV	A0RO	A08Z	A0RV	A0DP	A0EX	A15R	A0FD	A0ES	A0BM	A0EU	A12X	A146	A0CD	A0BQ	A04A	A0CT	A0TZ	A03L	A1AK	A0E1	A0H7	A0FS	A0BS	A08O	A12H	A15E	A0W4
+hsa-let-7a-1	11.835815644832	12.8979316315316	12.3077264364518	12.0392931397056	13.3909710853051	12.3403716402942	12.4376972179566	12.528040711661	12.2303801926699	12.6698204160879	12.3358436987028	13.283579314906	12.2545269164956	11.0027849408173	12.7180017316901	12.958885782004	13.0262067041266	12.5641094680723	13.214384243417	12.5613010497507	12.7410885464923	12.5157778750768	12.0771217875159	11.6044426063893	11.9484169118454	13.1688269239202	11.9852589148499	12.0611652889261	12.1699609041276	12.1082430789922	11.4721931082866	12.2143406795753	11.7298015940342	12.8269098566174	12.5541123849918	13.1164053217407	12.0576069283974	12.1258627103158	12.9769769526979	12.2464294167105	12.935679861189	12.5224607623743	11.8033907845383	13.6250047449906	12.9710597058414	11.9524015329101	11.9643092845062	12.4337777389146	12.2591456619297	11.899452911699	12.2690683740472	12.9051652356923	13.8097500464211	12.4909070414256	11.476631483493	12.125726246115	11.8013559931218	12.90672777347	12.9121508997441	12.646731196011	13.0203905886699	11.8505928139576	11.9101755790094	12.5098904372521	12.6277921183386	11.8734628861699	11.2584370234828	12.7932476587228	12.2853558238226	12.1584795418384	13.5866887886824	12.6408103571907	12.8247166942501	11.9986777834229	12.2324659869663	11.7282351422921	13.1980786052157	13.435808121704	13.2468454441825	14.0556259530982	12.3180235040514	12.3590488164776	13.6418981566633	12.5762375554089	12.5119624993839	13.5886481666608	12.9417838114616	13.114541961399	12.8179933345004	13.3868570962932	12.1948957168744	14.5078462176913	13.3142198736859	12.5177726990162	12.601971095026	12.8796150297288	13.4859899617788	12.9242557157767	11.7321287260556	14.1550291103822	12.9888402733454	13.5322812102328	12.6376896392974	13.0582599753685	12.4371763968368	12.575002269939	13.0294551646997	12.6698416766358	13.1401486820964	12.1038074605682	14.4556905908099	12.8310864359028	12.6691296829104	11.2072542952068	13.5025565379401	12.3306612538583	12.2852046642376	13.1164238648885	13.0957726835188	12.5177800103776	12.1666243123237	12.4925684484592	13.072977675241	12.6147859638672	12.3325762486501	12.538261803936	13.1347393509546	12.4600081617071	13.0472908786287	12.1346854573122	12.6368192500136	13.7109654018677	12.7967363804469	12.9731614253651	12.4004781587925	12.4773843956401	13.5449670478594	12.088458619634	12.5449112711427	12.0454816886557	11.9447971168238	13.2817259831617	13.8150067417114	12.8462689163501	13.3782321356653	13.5706824924471	13.1443570820654	13.7318960213208	13.2146252444769	12.1358657183454
+hsa-let-7a-2	12.8510467162388	13.9008691660534	13.2903246797872	13.0108071298356	14.3898160002792	13.3598599485471	13.4058889250225	13.5186287234223	13.239471139603	13.6546079568221	13.3281765679511	14.2868970617014	13.2534389472357	12.0341067632947	13.7181234318919	13.9163609956156	14.0316053763626	13.534778351019	14.1900960713661	13.5406263344858	13.7267848595918	13.5112138002715	13.0113030770216	12.582067014834	12.9327780123148	14.1607491198495	13.04277267833	13.053684309033	13.1151871854467	13.1200557975254	12.4757689369628	13.1902241389071	12.7442374229544	13.8124513743585	13.5473907164616	14.121939528459	12.9931488188471	13.1372265910567	13.9943336227508	13.2624725513099	13.9375452218172	13.5436868041695	12.8039225752631	14.6243929401949	13.9154550945364	12.9109658374062	12.9346256317059	13.4057857879378	13.2397708290292	12.8944221569957	13.258631450177	13.9019553737205	14.8125500879933	13.4648740176653	12.4964430137695	13.112918557854	12.7824862410682	13.9040477417783	13.9206011159376	13.6400566985177	14.0131672159521	12.8638834602935	12.9026603898395	13.53737283824	13.6224780052709	12.8667133906197	12.2194056706161	13.7683996319255	13.2774872917926	13.1638754316866	14.5897275420406	13.6283161573614	13.8105637860229	13.0133905915677	13.2345385272464	12.7023469943537	14.2073575219817	14.4341512537246	14.2608021912495	15.0564299860635	13.3176929266108	13.3526065378516	14.6551269765501	13.5638458650866	13.4848891702615	14.5970318136471	13.9423715870008	14.1231834822795	13.8006464003448	14.3946090988683	13.1904216753305	15.513832431795	14.3103368023103	13.5310267577097	13.6155489660785	13.9038196653086	14.4944540989537	13.9297258683847	12.6927910974421	15.1526483869374	13.9910977456565	14.5243502553496	13.626443489323	14.0482234272308	13.4348317028578	13.5572469560714	14.0266181258113	13.6364567379271	14.1606305688987	13.1031589585812	15.4680901164274	13.8323061862042	13.6805327042812	12.207542967005	14.4902944471651	13.3273393665033	13.2163107364144	14.1288345569203	14.0989966830845	13.4992863285605	13.1934858604175	13.4777947114611	14.072546517103	13.6133449555338	13.3203903915429	13.527538520698	14.1407073970432	13.4486359359513	14.0588814035228	13.1061274401441	13.6363645284664	14.7152094699469	13.7941428046372	13.9684303163379	13.3964658814629	13.4818648498212	14.5463987731237	13.0669164550544	13.5483545742366	13.0522274742862	12.9520187553994	14.2687701040106	14.8019274165983	13.8329529571243	14.3517861474061	14.5669131681569	14.1457167855549	14.7346161976019	14.2145905566641	13.133010291234
+hsa-let-7a-3	11.9188113263646	12.9127259302698	12.3006247974952	12.0814070379743	13.4222777526341	12.3932000195956	12.4644795491056	12.541838588839	12.2921490197409	12.6828137293762	12.3282497807618	13.3009587313254	12.3015356619859	11.0505072978821	12.7754244706727	12.9685449551173	13.0612653111573	12.5861847628484	13.2297657531657	12.5458650275037	12.7421400256375	12.5218409342801	12.110159449095	11.6355669451926	11.9231786521269	13.1681080624474	12.0395647921155	12.0900270238981	12.1857080516192	12.1297276530906	11.4971884500862	12.2682696569205	11.8171858748223	12.8275068287379	12.6090255463153	13.1327016097868	12.0135476460917	12.1931321612147	13.0060217120902	12.257297574263	12.9589046578485	12.5613318692041	11.8312046656333	13.6203228630789	12.9993713038494	11.9458904306211	11.9899880031614	12.4394353737766	12.2947917795636	11.8927413328591	12.262940891449	12.9090692267439	13.8061865881553	12.4803705694627	11.5019695889328	12.1612237274897	11.8258325204087	12.9073003964868	12.9325606292688	12.6476850177306	13.0306791947965	11.9153897057061	11.9396503655636	12.5880183119704	12.6426523379293	11.9468905675681	11.2531806141358	12.7916525840584	12.3119758402727	12.162422873183	13.6012391779405	12.6300831885916	12.8697706305706	12.0030995179542	12.2419376537068	11.7787741898134	13.2283603365095	13.4272321296134	13.2624726500962	14.0586589139194	12.3489800703899	12.3661583629114	13.6661018279769	12.5864203078369	12.5201915653868	13.6078112610273	12.9825890909643	13.150603618056	12.8306968859863	13.3899120366426	12.2171994682693	14.5054353590603	13.3179869545204	12.529576011803	12.6325562171454	12.9125269510957	13.5065396167196	12.9456340797849	11.7117573963729	14.1435037597561	13.0013981916903	13.5574199005071	12.6760263086857	13.0636516594609	12.4507060860912	12.5839430837966	13.0231612443406	12.6686154685462	13.1694256615889	12.1054444840989	14.4684143666664	12.8018462651211	12.7316865673545	11.2560753580957	13.4605999389698	12.4072865736696	12.274411738312	13.1294869828977	13.084409326191	12.5190489273343	12.1912558750758	12.525912113671	13.0642656835088	12.6349106576849	12.3724437023816	12.5466082146998	13.1560009662389	12.4705379457462	13.0606900734556	12.1363254827069	12.6617001360736	13.7191048101041	12.834576149257	12.9520235483172	12.415141611462	12.4761765129165	13.5482602895982	12.1622162796363	12.5902013816536	12.0832874139104	12.0397553147605	13.2817517400538	13.805422223771	12.8930109453541	13.3810932391035	13.5758113686968	13.1690944903276	13.7467717483067	13.2280673861696	12.1863896867711
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/mrna.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,201 @@
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+ZNF680	3.35263746236406	3.63714210815612	3.63387946506984	3.9872332043466	3.26496893567681	4.11082316951401	2.39417922669289	4.24646598022809	3.87801679760445	3.42657094799141	3.62091895741204	3.72490145612389	5.04941970814444	2.80246088153209	3.7515932219171	3.24603570399509	4.7866372536847	3.51244761291082	4.23292853422188	3.6454137127995	3.03376521485887	3.33230691261003	3.59810789186405	3.79445449524008	3.8980635576697	1.82517603173324	3.50579374007436	3.32094172332591	3.30428595428524	3.33061453669856	3.22786138185472	2.43800130318934	3.27842682886915	1.85588151918903	4.16447264922781	4.17575873922241	3.20955457613478	3.74211749702222	2.58172857123793	3.66482276748164	3.76112053611092	2.99668385922322	4.2087890730911	4.37273363238987	3.56623839007023	3.55457510368163	5.29802317209845	3.70593513664335	4.20731143892182	4.84952826560253	3.44547023047675	3.57033464859273	4.51203625103925	4.28399710101546	2.76177906578611	3.94207454423691	3.20980540343748	3.93592643086086	4.95453828945286	3.08231555386026	3.61857375101501	3.29030382554092	3.55579576047408	2.49530326176555	3.88840144469572	4.30821805914547	6.01179555775016	4.02362704113911	6.25602373076316	3.73007475222299	4.15074513582839	4.25165035403992	3.79298364443206	4.5231713085715	3.57150299466993	3.54964711799377	3.71217906834465	4.24006728719358	4.40938992300006	4.45286490706087	5.59970912560354	4.44104884670866	4.26982830156181	4.32090078352971	5.07187437143794	4.68199673750916	4.27263754466315	3.27246599832286	4.19866151694147	3.95744854718022	3.05106310596844	3.54379017920574	5.51333679885505	4.00827038424152	4.95799015584768	4.36760309368419	2.67166488728712	5.07360525406922	4.5517818809124	5.25970291032257	3.50049106744817	4.60080473930441	4.01944642711832	4.03138914840184	4.11368634179032	3.37129920539867	5.44574350850079	3.54196708068998	4.54772500133368	4.72529875581	4.69490005918295	3.50815450445302	4.63075474560243	3.61319427725242	4.48422047958296	5.21613802715297	4.6669059773545	4.60186070212541	4.04564238941197	4.76773133223448	4.63762370834167	4.88108367138654	5.48401038971853	6.24149037038521	4.41357983651226	4.09264099031607	4.74181179212416	3.81188995525551	4.3060575188394	4.90872250626041	4.76863546425624	4.1566205626222	4.99494281432505	3.79365492709902	5.20055913893821	4.32983082215666	3.88765711732449	2.69368605127546	3.27349604573502	4.92895876805411	4.21933242062932	4.02588389675279	3.82124880090162	4.39706290341274	5.36204896132871	4.69251834712675	5.63033289647241	4.96159123200293	4.92024238549147	5.30841901934846
+PBX1	7.88092300923167	7.80708187253919	7.44171248175659	8.0212527518951	8.13855259215621	7.61413438942804	7.17748025427613	5.62811436988707	6.84891643489385	7.23493173886896	7.96835111075809	5.72793686695129	7.54942987431732	8.63517540073317	6.6128960541713	8.90740330848911	5.8115106293884	6.5400847918313	8.24590348471777	8.87999334169951	6.93267831832082	6.63958344228165	8.46943473362153	7.37988529639546	7.05463676342716	6.96635971958698	6.55485940177739	7.07793027398837	6.01789381026174	6.80082042127886	8.45292250160292	7.05364624071104	7.81584106963708	5.52947172642586	7.78851942541371	8.82503919313851	7.98038211742487	8.34654929178269	8.12969680659069	6.81876048942641	8.37228760185987	5.02576998154109	7.83523262357786	5.99016450772375	8.31346885302789	7.66397177779925	7.32623092725696	6.29819254219003	10.2371247564296	6.66947408589776	7.16788317759424	7.89603954358955	10.5682351407128	9.4418238788346	7.34983835585588	9.05696166939158	8.84622167728727	9.07793462636245	8.61503794813458	7.67527670975958	7.73880489243302	8.79825113099322	6.74981695836587	8.28564162855428	7.2745050045141	9.14319368994871	8.89414556734336	8.7119677045851	7.06156537452887	8.0570407604451	8.43714685990108	7.89744474441131	9.70875209859971	8.23903870052126	8.6113468139873	7.64748159686987	8.27102364101787	10.1326114407645	7.76824517396916	8.49238496883636	8.06378077204808	8.87801616357628	9.24513372138269	6.29038428609272	8.49162627539797	9.02135068753964	9.23904993911955	8.02758804993205	9.60578772299973	8.96701371982351	9.10639066065331	9.08086503397672	10.2186061652581	8.64258068345196	8.17412149805167	8.84877094321941	7.83420168074237	8.40860321657922	7.92330383963574	8.27907379419102	8.05144821049666	8.60998991615305	9.53104676351939	8.30472467428088	9.03270735815495	7.53948006461291	7.88040715961043	8.73432085581719	9.14238722041573	8.59346771376266	8.96758075718822	7.24756077504832	8.08064258342968	10.6743628490596	8.61337981996603	9.59083818271245	8.74741708821279	8.03787618449019	8.57840118222964	8.60517760752556	8.12653187791195	9.18569705017285	9.88818491217851	8.65850438380719	8.48141593402946	8.62579506032136	8.56800463870092	8.3814963757479	8.77040213938239	8.23176669885437	8.48192355434204	8.23479236458186	8.58090937273408	8.67473384700724	8.19726389989026	9.56555174927736	8.50729470060556	8.63033688260066	9.2715258762283	9.86478079918749	9.28205756116671	8.73341376403773	8.85519815112409	8.63851788999465	8.70910184492883	9.12481023020771	8.8450850082005	7.635796561253	8.21435517587345	8.40826764568451
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/param_integration_mixOmics.txt	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,9 @@
+Nombre de variables à sélectionner :
+mrna 50
+mirna 40
+protein 40
+
+ncomp = 2
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/protein.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,143 @@
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+p70S6K_pT389	-0.173937623101939	0.292625342380577	-0.159280275763519	-0.167167192246457	-0.336897518761597	0.00958652495650858	0.182729472891014	1.64439290417385	0.501603620476819	0.0815950265354074	-0.0542127107372028	0.058385948733544	-0.0234313581957826	0.446765693968282	-0.0668372101975365	-0.0282361188229281	-0.271574869303904	-0.0954171137385429	-0.00532181007427046	0.14339376297623	-0.064699839774018	-0.0740423337571567	-0.306738578679238	0.241383846683577	0.0525880737226322	-0.0931295923140376	-0.166855463733774	0.69937480085389	-0.0810780419511271	-0.208099041064807	-0.119984466608552	-0.165259383743048	-0.271261089548283	-0.126011460760865	-0.27442563189599	0.0305962272566113	0.0525421496425655	9.0380315176386e-05	0.252531324426889	-0.00598246694368121	0.249537015567617	-0.23919334832047	-0.171739079355195	0.220472697695642	-0.277533901488385	0.214944371372796	0.0827067713409984	-0.40685515527085	0.2712843586267	-0.165394791987977	0.30325665347726	-0.407935140324075	-0.148317322040501	0.448390755346916	0.251027737499629	-0.033313480700993	0.374256528639283	-0.293599317137505	-0.314898154046768	-0.0731218587306243	0.170419260247437	0.00277674324968979	-0.282709195444448	-0.0394972967422303	-0.217423416006663	-0.150792400292058	0.231106113672625	-0.160033141054258	0.0578279626844211	-0.126249263114704	-0.0956525565877587	-0.304565132140042	-0.132373874858	1.2904549211442	-0.0896064911802957	0.0676746611220023	0.0869818273237415	-0.0103275229624651	-0.156398216304695	-0.110316011028688	0.952489934761324	-0.524691780756042	1.37802555933736	0.0612034737186006	-0.0660314636443711	-0.350867228456025	-0.0624883466834733	-0.295113351275058	-0.255314321654248	-0.337834361862143	-0.0820111415689679	-0.233755920507857	0.0081213338771815	0.0260396345135386	-0.415610733840279	-0.008961135180234	-0.0620483984279374	0.0293144839141122	-0.103204520317726	0.106211780262317	0.148135691993841	0.0659558418013219	-0.027236448621285	-0.139272289580248	-0.362672057693408	-0.212356191434831	0.0703287212567374	0.746023439247047	-0.245076499354356	-0.41889753189482	1.08029239253375	-0.0846511718001043	-0.331095895312152	0.405342580790207	-0.181375153339956	0.630258672241538	-0.0833766899922277	-0.508446157134899	-0.161787784767184	0.415757132756226	0.520044564750124	-0.57968803162957	-0.393369855156248	-0.20089667433676	0.160444144072671	0.275351896336189	0.175587311874847	-0.115598137206496	-0.0459282751542969	-0.202990163930018	-0.320978694438516	0.81681700062512	1.00412813748136	-0.132931268945527	-0.394440780921623	0.105891929070285	-0.33544897747058	-0.28462358351294	-0.304431353117818	0.317166643672133	-0.0894721069122625	-0.113328908339336	-0.172632102721044	0.258357454347293	-0.147852895248459	-0.131522752648169	0.525965804716234	-0.185404458371424	-0.293370909569497	-0.216363986228487
+p90RSK_pT359_S363	-0.15741890771665	0.503641937086014	0.353103707811045	-0.146854930363834	0.634387055450553	0.0579433794837493	0.226068767326157	-0.398537940718849	-0.270609087851135	-0.516343082491496	0.320733866943247	-0.581402016743339	0.569318078056836	0.280570996991129	0.00199920883066929	0.000468711110012787	0.258500633191248	-0.253413409637345	0.846676212937588	0.128084860583267	0.159432186456393	0.376784782277835	-0.0694296343399743	-0.422859722093256	0.192103478286706	-0.089658842843461	-0.0146763109739306	-0.145693631966013	-0.469843360809856	-0.0700116516868287	-0.445002953802796	0.0825570524270689	0.27060168749142	-0.159184663225609	0.171966157769463	0.626126378186317	-0.0954837387989864	-0.0753730462194948	-0.0179605025001015	-0.238534247732298	0.931037565200879	-0.482341074979006	-0.206527782858493	-0.344980548178661	0.153203462260316	-0.119845434373024	0.0625322332512702	-0.244549923897792	0.0973994675355128	-0.0568334213797961	0.0909556254515569	0.304880400479178	0.322621215733005	0.0131197127721032	-0.0925694642854916	-0.212856557358386	-0.00661857185237746	0.0243337838683726	0.0277681812799735	0.0129589987595134	-0.753121614133206	0.197358871901196	-0.11029060468985	-0.23058471285409	-0.0167941039826035	-0.131859069194122	-0.142454191572913	-0.240619902083831	-0.456026783573473	-0.115758687472636	0.120209139314941	0.169955766448218	0.408111725209331	-0.238331593788539	-0.129847965244069	-0.133541704949751	0.0675045774388183	0.611913958337335	0.174902264298335	0.00292919392416219	-0.223947651138999	-0.363831591673215	-0.423511193750844	0.430174651585807	-0.0500570485844045	0.278655327903113	0.35704216515922	0.140726667446533	-0.0646879570248517	-0.0476114837371859	0.0973145489728668	-0.29474058971041	-0.0317919084424805	-0.201291885326395	0.331266886972276	-0.361543973894197	-0.456916525374331	-0.420486230769741	0.0565524609621154	-0.534364831076986	-0.477963887502463	-0.111135593558034	-0.336545756741778	0.39402165635646	-0.557989882486459	0.210415326066138	0.153776778632895	-0.592049600135786	0.248457626350141	-0.265291778295264	0.114093691624581	0.0730677977129317	0.277484232815996	-0.077070954438856	0.0422573431361314	0.0613540223881014	-0.243225460199641	-0.100373538891352	-0.167003187059263	-0.0885501959998768	0.437695280438562	-0.376505152963483	0.127740578238549	-0.805574852578013	0.164544709203625	-0.222613867172458	-0.0809826178572361	-0.272405706434259	0.265514707151225	-0.606985738877119	-0.0434821942604194	-0.333881996691063	-0.372191000350558	0.296588233235383	0.289022442274399	0.616225890520622	-0.394589141092651	-0.282377091712343	-0.407711600517251	-0.136167819381701	-0.112494300840799	-0.549216273251539	-0.374335708293407	-0.15220899382468	0.0233077316201378	-0.346342514483715	0.235879837093735	0.0482028464523092	-0.11326497662798	0.210828713540271
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/response_var.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,3 @@
+Basal
+Her2
+LumA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data/var_interest.tsv	Tue Sep 07 10:40:08 2021 +0000
@@ -0,0 +1,6 @@
+NDRG2
+CCDC113
+hsa-let-7a-1
+hsa-let-7a-2
+14-3-3_epsilon
+4E-BP1
--- a/macros_mixomics.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/macros_mixomics.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@TOOL_VERSION@">6.12</token>
+    <token name="@TOOL_VERSION@">6.14</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">bioconductor-mixomics</requirement>
@@ -38,4 +38,4 @@
             <citation type="doi">10.18129/B9.bioc.mixOmics</citation>
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
--- a/macros_viscorvar.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/macros_viscorvar.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@TOOL_VERSION@">0.7</token>
+    <token name="@TOOL_VERSION@">0.9</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">r-viscorvar</requirement>
@@ -37,4 +37,4 @@
             <citation type="doi">10.18129/B9.bioc.mixOmics</citation> -->
         </citations>
     </xml>
-</macros>
\ No newline at end of file
+</macros>
--- a/mixomics_blocksplsda.R	Tue Nov 17 13:01:44 2020 +0000
+++ b/mixomics_blocksplsda.R	Tue Sep 07 10:40:08 2021 +0000
@@ -22,7 +22,6 @@
 parser$add_argument('--correlation', dest='correlation', action="store_true",
                     help="Add correlation between all blocks")
 parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme")
-parser$add_argument('--mode', dest='mode', default="regression", help="Mode")
 parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100,
                     help="Maximum number of iterations")
 parser$add_argument('--scale', dest='scale', action="store_true",
@@ -54,8 +53,6 @@
 print(args$correlation)
 print("Scheme:")
 print(args$scheme)
-print("Mode:")
-print(args$mode)
 print("Max nb of iterations:")
 print(args$maxiter)
 print("Scale:")
@@ -165,7 +162,6 @@
                                 keepX = keepX,
                                 design = design,
                                 scheme = args$scheme,
-                                mode = args$mode,
                                 scale = args$scale,
                                 init = args$init,
                                 tol = args$tol,
--- a/mixomics_blocksplsda.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/mixomics_blocksplsda.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_blocksplsda" name="mixOmics block.splsda" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
 
     <description>performs N-integration and feature selection with Projection to Latent Structures models (PLS) with sparse Discriminant Analysis</description>
 
@@ -33,7 +33,6 @@
         --ncomp ${adv.ncomp}
         ${correlation}
         ##--scheme ${adv.scheme}
-        ##--mode ${adv.mode}
         --maxiter ${adv.maxiter}
         ##${adv.scale}
         --scale ## always activated hidden param
@@ -79,12 +78,6 @@
                 <option value="horst" selected="true">horst</option>
                 <option value="factorial"            >factorial</option>
                 <option value="centroid"             >centroid</option>
-            </param>
-            <param name="mode" type="select" label="Mode">
-                <option value="regression" selected="true">regression</option>
-                <option value="canonical"                 >canonical</option>
-                <option value="invariant"                 >invariant</option>
-                <option value="classic"                   >classic</option>
             </param> -->
             <param name="maxiter" type="integer" value="100" min="1"
                    label="Maximum number of iterations"
@@ -148,8 +141,8 @@
 
 The blocks.splsda function is part of the mixOmics package for exploration and integration of omics datasets.
 This data integration takes as input parameters different omics datasets
-(transcriptomic, metabolomic, metagenomic, ...) and a response variable (e.g. for a sample, the value of the response
-variable is equal to « Treated »  or « Control »). This data integration returns, for each omics dataset, variables
+(transcriptomics, metabolomics, metagenomics, ...) and a response variable (e.g. for a sample, the value of the response
+variable is equal to « Treated »  or « Control »). This data integration is performed fo the scheme "horst" and the mode "regression". This data integration returns, for each omics dataset, variables
 which are correlated with the variables of the other omic datasets and the response variable. The other functions of
 this pipeline allow visualizing this correlated variables thanks to correlation circles and networks.
 
@@ -198,9 +191,6 @@
 The first row contains the metadata column names.
 The number of rows in the metadata file must be the same than the number of rows in the block data file, and the variables need to be in the same order. If a metadata file is provided, block.splsda output will be appended as new columns, otherwise a new file will be created.
 
-Variables metadata files are optional.
-If a file is provided, output metadata will be appended to the input file, otherwise a new output file will be created.
-
 
 Global input files:
 -------------------
@@ -215,47 +205,14 @@
 Samples metadata is in tabular format (.tsv).
 The first column contains the sample names.
 The first row contains the metadata column names.
-Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for integration.
+Samples names must be in the same order in samples metadata (transposed) and all the blocks. One of the column (the last by default) must contain the samples groups for data integration.
 
 ----------
 Parameters
 ----------
 
-For each block (min 2 blocks):
-------------------------------
-
-Block name
-    Name of the block. If not provided, this will default to the input filename
-
 Number of variables to select for each component
-    If set to 0 (default), all variables will be considered in the model
-
-Global parameters:
-------------------
-
-Sample description column number
-
-Number of components to include in the model
-
-Correlation between all blocks
-
-Advanced options:
------------------
-
-Scheme
-
-Mode
-
-Maximum number of iterations
-
-Scale
-
-Init
-
-Convergence stopping value (tol)
-
-Near zero var
-
+   tune.block.splsda can be used to set the number of variables to select on each component
 
 @HELP_MANUAL@
 
--- a/mixomics_plotindiv.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/mixomics_plotindiv.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
 
     <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description>
 
@@ -84,18 +84,11 @@
 | 1 : Rdata block.splsda output |   Rdata    |
 +-------------------------------+------------+
 
+
 ----------
 Parameters
 ----------
 
-Advanced options:
-=================
-
-Plot legend
-
-Plot ellipse plots
-
-
 @HELP_MANUAL@
 
 ------------
@@ -109,4 +102,4 @@
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>
--- a/mixomics_plotvar.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/mixomics_plotvar.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy2" profile="16.04" workflow_compatible="true">
+<tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy0" profile="16.04" workflow_compatible="true">
 
     <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description>
 
@@ -90,14 +90,6 @@
 Parameters
 ----------
 
-Advanced options:
-=================
-
-Plot legend
-
-Cut-off
-
-
 @HELP_MANUAL@
 
 ------------
@@ -105,10 +97,10 @@
 ------------
 
 plotVar.pdf
-    A pdf file with scatter plots for variables
+    A pdf file with scatter plots for the variables
 
     ]]></help>
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>
--- a/viscorvar_circlecor.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_circlecor.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -26,8 +26,6 @@
         --output_var ${output_var}
         --output_pdf ${output_pdf}
 
-        @COMMAND_LOG_EXIT@
-
     ]]></command>
     <inputs>
         <param name="input_rdata" type="data" format="rdata"
@@ -35,7 +33,7 @@
                help="this is the RData output file from the matCorAddVar function"/>
         <param name="blocks_vec_list" type="data" format="tabular"
                label="List of blocks vector."
-               help="output *_blocks_comb.tsv file from matCorAddVar."/>
+               help="output *_blocks_comb.tsv file from the matCorAddVar function."/>
         <param name="select_blocks" type="select"
                label="Blocks"
                help="each element of List of blocks vector contain blocks for which selected variables can
@@ -48,7 +46,7 @@
         </param>
         <param name="responses_var_list" type="data" format="tabular"
                label="List of response variables."
-               help="output *_response_var.tsv file from matCorAddVar"/>
+               help="output *_response_var.tsv file from the matCorAddVar function"/>
         <param name="select_responses_var" type="select" display="checkboxes"
                multiple="true" label="Response variables"
                help="choose the response variables which will be plotted in the correlation circle">
@@ -89,11 +87,10 @@
 Description
 -----------
 
-This tool allows visualizing variables of omics datasets which are correlated with
-the response variables thanks to correlation circles. The determination of the omics
-datasets which can be visualized is made by the tool matCorAddVar. This tool performs
+This tool allows visualizing variables of omics datasets which are correlated with response variables thanks to correlation circles. The determination of the omics
+datasets which can be visualized is made by the matCorAddVar tool. This tool performs
 a zoom in a rectangle to retrieve omics datasets variables which are correlated with a
-response variable. 
+response variable.
 
 -----------------
 Workflow position
@@ -126,9 +123,9 @@
 +===========================================================+===========+
 | 1 : Rdata visCorVar.matCorAddVar output                   |  rdata    |
 +-----------------------------------------------------------+-----------+
-| 2 : ``*``_blocks_comb.tsv visCorVar.matCorAddVar output   |  tabular  |
+| 2 : \*_blocks_comb.tsv visCorVar.matCorAddVar output      |  tabular  |
 +-----------------------------------------------------------+-----------+
-| 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output  |  tabular  |
+| 3 : \*_response_var.tsv visCorVar.matCorAddVar output     |  tabular  |
 +-----------------------------------------------------------+-----------+
 
 ----------
@@ -145,10 +142,10 @@
     Correlation circle pdf file
 
 viscorvar_circlecor_selected_var.tsv
-	List of variables selected in the correlation circle
+	List of selected variables which are contained in a rectangle of the correlation circle
 
     ]]></help>
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>
--- a/viscorvar_computematsimilarity.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_computematsimilarity.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -15,11 +15,9 @@
         @COMMAND_RSCRIPT@/viscorvar_computematsimilarity.R
 
         --input_rdata ${input_rdata}
-        
+
         --output_rdata ${output_rdata}
 
-        @COMMAND_LOG_EXIT@
-
     ]]></command>
     <inputs>
         <param name="input_rdata" type="data" format="rdata"
@@ -93,10 +91,12 @@
 ------------
 
 viscorvar_computematsimilarity_output.RData
-    RData output
+    | RData output
+    | Contains the `computeMatSimilarity_result` R object containing the result of the computeMatSimilarity function
+
 
     ]]></help>
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>
--- a/viscorvar_matcoraddvar.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_matcoraddvar.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -27,8 +27,6 @@
         --output_response_var ${output_response_var}
         --output_blocks_comb ${output_blocks_comb}
 
-        @COMMAND_LOG_EXIT@
-
     ]]></command>
 
     <inputs>
@@ -37,7 +35,7 @@
                help="this is the RData output file from the block.splsda function" />
         <param name="block_Y" type="data" format="tabular"
                label="Block Y"
-               help="Block Y is a table. A column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). For the file structure, see below in the section Input files" />
+               help="Block Y is a table. A column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). For the file structure, see below in the section Input files" />
         <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
         <param name="var_of_interest_file" type="data" format="txt" optional="true"
                label="Variables of interest (Optional)"
@@ -119,7 +117,7 @@
 Block Y is in tabular format (.tsv).
 This table contains the name of the samples in the first column.
 The other columns correspond to phenotypes.
-For each of these other columns, a column determines which sample is associated with a phenotype (value equals to 1) or not (value equals to 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order.
+For each of these other columns, a column corresponds to a phenotype and determines which sample is associated with this phenotype or not (value equals to 1 or 0). The names of the samples in Block Y (transposed), in the sample metadata (transposed) and for all datasets have to be in the same order.
 
 3. Variables of interest structure
 All the variables of interest are in the same column.
@@ -135,16 +133,14 @@
 ------------
 
 viscorvar_matcoraddvar_output.RData
-    RData output
-
-viscorvar_matcoraddvar_response_var.tsv
-
+    | RData output
+    | Contains the `matCorAddVar_result` R object containing the result of the matCorAddVar function
 
 viscorvar_matcoraddvar_blocks_comb.tsv
-
+    | viscorvar_matcoraddvar_blocks_comb.tsv contains the block names whose correlation circles can be overlaid
 
     ]]></help>
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>
--- a/viscorvar_networkvar.R	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_networkvar.R	Tue Sep 07 10:40:08 2021 +0000
@@ -66,8 +66,9 @@
 print("names_response_variables:")
 print(names_response_variables)
 
-res_networkVar = networkVar(res_compute_mat_similarity = res_compute_mat_similarity,
-                            names_block_variables = names_block_variables,
+res_networkVar = networkVar(res_compute_mat = res_compute_mat_similarity,
+                            type_cor = "similarity",
+                            names_selected_variables = names_block_variables,
                             names_response_variables = names_response_variables,
                             cutoff = 0)
 
@@ -75,4 +76,4 @@
 print("res_networkVar:")
 print(res_networkVar)
 
-write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml")
\ No newline at end of file
+write.graph(res_networkVar$gR, file = args$output_graph, format = "graphml")
--- a/viscorvar_networkvar.xml	Tue Nov 17 13:01:44 2020 +0000
+++ b/viscorvar_networkvar.xml	Tue Sep 07 10:40:08 2021 +0000
@@ -20,17 +20,15 @@
 
         --output_graph ${output_graph}
 
-        @COMMAND_LOG_EXIT@
+    ]]></command>
 
-    ]]></command>
-   
     <inputs>
         <param name="mat_similarity_rdata" type="data" format="rdata"
                label="this is the RData output file from the computeMatSimilarity function"
-               help="output RData file from computeMatSimilarity"/>
+               help="output RData file from the computeMatSimilarity function"/>
         <param name="var_list_file" type="data" format="tabular"
                label="Variables list file"
-               help="selected variables output tabular file from circleCor"/>
+               help="selected variables output tabular file from the circleCor function"/>
 
         <!-- Fichier avec noms de gènes/variables, donné par l'utilisateur -->
         <!-- <param name="var_of_interest_file" type="data" format="txt" optional="true"
@@ -39,7 +37,7 @@
 
         <param name="response_var_list" type="data" format="tabular"
                label="List of response variables"
-               help="output *_response_var.tsv file from matCorAddVar"/>
+               help="output *_response_var.tsv file from the matCorAddVar function"/>
         <param name="select_response_var" type="select" display="checkboxes" multiple="true"
                label="Response variables"
                help="response variables that will be plotted in the network">
@@ -72,10 +70,10 @@
 -----------
 
 This tool creates a network of correlated variables for omics datasets. The determination of
-the omics datasets which can be visualized is made by the tool matCorAddVar. This network can
+the omics datasets which can be visualized is made by the matCorAddVar tool. This network can
 be exported to graphml format and visualized with Cytoscape. The link between two variables
 is associated with the correlation between two variables : a threshold can be used in
-Cytoscape to get a network of variables whose correlation is greater than this threshold
+Cytoscape to get a network of variables whose correlations are greater than this threshold
 in absolute value.
 
 -----------------
@@ -105,9 +103,9 @@
 +===========================================================+===========+
 | 1 : Rdata visCorVar.computeMatSimilarity output           |  rdata    |
 +-----------------------------------------------------------+-----------+
-| 2 : ``*``_selected_var.tsv visCorVar.circleCor output     |  tabular  |
+| 2 : \*_selected_var.tsv visCorVar.circleCor output        |  tabular  |
 +-----------------------------------------------------------+-----------+
-| 3 : ``*``_response_var.tsv visCorVar.matCorAddVar output  |  tabular  |
+| 3 : \*_response_var.tsv visCorVar.matCorAddVar output     |  tabular  |
 +-----------------------------------------------------------+-----------+
 
 ----------
@@ -127,4 +125,4 @@
 
     <expand macro="citations" />
 
-</tool>
\ No newline at end of file
+</tool>