Mercurial > repos > eschen42 > w4mclassfilter

changeset 16:aae9fa9a7d4d draft default tip

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca-dirty"
author eschen42
date Thu, 11 Mar 2021 21:12:46 +0000
parents f9cb2244fd01
children
files test-data/expected_dataMatrix.tsv test-data/expected_sampleMetadata.tsv test-data/expected_variableMetadata.tsv test-data/input_med1_dm.tsv test-data/input_med1_sm.tsv test-data/input_med1_vm.tsv
diffstat 6 files changed, 51 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/expected_dataMatrix.tsv	Thu Mar 11 21:07:10 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-	HU_017	HU_034	HU_078	HU_091	HU_093	HU_099	HU_130	HU_134	HU_138
-HMDB00191	560002	575790	785428	645785	591569	960658	639437	1092885	1409045
-HMDB00208	747080	595872	3143654	4059767	1433702	5593888	2477288	3346077	4230072
-HMDB00251	368600	94936	293988	352855	767894	268331	310918	1248919	577184
-HMDB00299	250551	456162	808657	614370	250403	768004	504108	1014041	1362408
-HMDB00512	525240	280560	556003	590779	209285	342532	569970	525240	246282
-HMDB00518	0	85944	129886	175800	13154	230242	440223	315368	10657
-HMDB00715	1252089	905408	5140022	2658555	814523	2558923	4184204	3865723	3236644
-HMDB01032	2569205	1604999	26222916	257139	675754	59906109	31151730	18648127	14989438
-HMDB01101	30689	52217	229568	4763576	3878773	976436	608298	1605075	72021
-HMDB01101.1	6877586	3158	4763576	3878773	976436	831937	1605075	72021	442510
-HMDB03193	76043	44943	173175	242549	57066	559869	339188	471368	262271
-HMDB04824	374028	539206	959381	605191	310260	1253319	477995	825691	1157093
-HMDB10348	47259	60885	168264	176500	76457	610110	279156	524468	451573
-HMDB13189	2644620	1661412	2755434	593863	837865	3526136	1608814	3446611	1941527
-HMDB59717	357351	301983	1028110	1530493	270027	1378535	808334	1132813	871209
--- a/test-data/expected_sampleMetadata.tsv	Thu Mar 11 21:07:10 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-sampleMetadata	injectionOrder	mode	age	bmi	gender
-HU_017	2	pos	41	23.03	M
-HU_034	9	pos	52	23.37	M
-HU_078	34	pos	46	25.18	M
-HU_091	42	pos	61	26.12	M
-HU_093	43	pos	53	21.71	M
-HU_099	46	pos	23	21.3	M
-HU_130	63	pos	33	26.06	M
-HU_134	67	pos	48	22.89	M
-HU_138	68	pos	42	21.88	M
--- a/test-data/expected_variableMetadata.tsv	Thu Mar 11 21:07:10 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-variableMetadata	name	mz	rt
-HMDB00191	loquor	650	600
-HMDB00208	loquimini	873	476
-HMDB00251	pasamur	500	423
-HMDB00299	bantur	700	500
-HMDB00512	pantur	900	543
-HMDB00518	loquoris	870	250
-HMDB00715	loquitur	725	900
-HMDB01032	loquimur	550	425
-HMDB01101	bar	150	300
-HMDB01101.1	baz	200	225
-HMDB03193	foo	100	200
-HMDB04824	loquantur	950	522
-HMDB10348	batur	300	275
-HMDB13189	baris	800	325
-HMDB59717	bamur	125	400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_med1_dm.tsv	Thu Mar 11 21:12:46 2021 +0000
@@ -0,0 +1,10 @@
+X	M70T1043	M70T61	M71T138	M71T1041	M71T377	M71T369	M71T364	M71T555	M71T581	M72T34_1	M72T54	M72T34_3	M73T1061	M73T1044	M73T32_1	M73T1096	M73T32_2	M73T1043	M74T1042_1	M74T33	M74T871	M74T876_2	M74T858	M74T34	M74T1033	M75T34	M75T505	M75T431	M76T1040	M77T537
+trtA_1	0	0	0.103676462792297	0	0	0	0.09826970333995	0	0	0	0.0303803032193031	0	0.00180737321564983	0.174619941309	0	0	0	0	0	0	0	0	0	0	0.219609447733449	0	0	0	0.0151151439275008	0.502704391270598
+trtA_2	0.1499611203546	0.243708505613103	0	0.04320144565955	0.0317311746973008	0.171306020866901	0	1.0677832262992	0.4890197262973	0.140208039060401	0.00253982134690034	0.0563798353136988	0	0.00346576229545015	0.0285671029685997	0.0256247716491007	0.818318427514498	0.2150061358386	0.1234949545399	0.0398841868243505	0	0.7407933477417	0	0.0476545410972502	0	0.112811564993098	0	0	0	0.251352195635299
+trtA_3	0.0424174908139001	0.121854252806552	0.0518382313961485	0.0864028913191	0.1222967572165	0.342612041733801	0.849339292282099	0.0147975909652498	3.869505334958	0.285443289823299	0	0.112759670627398	0.0300457862235994	0	0.6387333497781	0.411653240176999	0.0933267742982	0.0514902142761002	0.0463451483315485	0.183561229851001	0.528508602842599	0	0.1934182113026	0.420661197739499	0.439218895466897	0.0175408561815491	0	0	0.1265423906184	0
+trtB_1	0	0	0	0	0	1.5113745967984	0.1965394066799	0.0295951819304996	0	0.280416078120801	0.00507964269380068	0	0	0.00346576229545015	0	0.0256247716491007	0.0933267742982	0	0.0463451483315485	0.2933301023069	0	0	0	0.935782704287199	0.219609447733449	0.0175408561815491	0	0	0.0151151439275008	0.251352195635299
+trtB_2	0.124637442941602	0.414790130357598	0.140388243320103	0.357735292121102	0.0634623493946016	0	0	0	0.978039452594601	0.140208039060401	0	0.0563798353136988	0.220593700553497	0.0767204072380991	0.0571342059371993	0.0815161028168028	0.446741706469403	0.0514902142761002	0	0.0398841868243505	0	0	0	0.0476545410972502	0.761398854361399	0	1.086467693902	0	0	0.580225894218799
+trtB_3	0.0424174908139001	0.121854252806552	0.0518382313961485	0.04320144565955	0.0317311746973008	0.171306020866901	0.09826970333995	0.0147975909652498	0.4890197262973	0	0.00253982134690034	0.2357122484906	0.00180737321564983	0	0.0285671029685997	0	0	0.1029804285522	0.204744259308601	0	0	0	0	0	0	0.0422615246151992	0	0	0.2218306650343	0
+trtC_1	0	0.320143072543999	0.0518382313961485	0.7011594009854	1.9883459973714	1.8589982127458	1.1443146127588	0.269349110340201	1.2385296023128	0	0.730941378584301	0.640778164724498	0	0.0069315245909003	0.125735401747001	0.0512495432982014	0	0	0	0	0.0667424385274984	0.268514070203597	0.752261526391599	0	0.679179854411199	0.0175408561815491	0	0	0.0302302878550016	0.754715219586299
+trtC_2	0.0848349816278002	0.121854252806552	0.244624610443701	0	0	0	0	0	0.4890197262973	0.513858474098299	0	0.0563798353136988	0.00180737321564983	0.00346576229545015	0.0285671029685997	0.0256247716491007	0.1866535485964	0.3576876580278	0.0926902966630969	0.0797683736487009	0	0	0	0.0953090821945004	0	0.0350817123630982	0	1.900985710853	0.0151151439275008	0.251352195635299
+trtC_3	0.0424174908139001	0	0	0.04320144565955	0.0317311746973008	0.171306020866901	0.09826970333995	0.0147975909652498	0	0.140208039060401	0.00253982134690034	0	0.00361474643129966	0	0	0	0.0933267742982	0.0514902142761002	0.0463451483315485	0.0398841868243505	0	0	0	0.0476545410972502	0.219609447733449	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_med1_sm.tsv	Thu Mar 11 21:12:46 2021 +0000
@@ -0,0 +1,31 @@
+sampleMetadata	pcgroup	mz	rt
+M70T1043	10	70.0122929793033	1042.83709612962
+M70T61	183	70.0651210994061	61.3905354181062
+M71T138	134	70.7378907468715	137.798948287145
+M71T1041	89	70.9909558511769	1041.40508992281
+M71T377	35	71.0488173286188	376.931518857336
+M71T369	27	71.0488456490549	368.759546615083
+M71T364	45	71.0488487473802	364.081506343325
+M71T555	37	71.0489644640144	555.004553220191
+M71T581	44	71.0490430805114	581.198136872667
+M72T34_1	345	71.529455784918	33.7387759459325
+M72T54	353	72.0807228513553	54.4048259006589
+M72T34_3	345	72.0807426611777	33.8672738618788
+M73T1061	8	72.9367161649113	1060.80034606296
+M73T1044	10	72.9367229345106	1043.98726790638
+M73T32_1	85	72.9368652358215	31.7025769021219
+M73T1096	160	72.936874804031	1095.52504027727
+M73T32_2	85	73.0647299005977	32.166230277174
+M73T1043	10	73.1056566280053	1042.8817438948
+M74T1042_1	10	73.531470577532	1042.13833094273
+M74T33	345	73.5315669737491	33.3902011282139
+M74T871	29	73.7524028205993	871.313876430572
+M74T876_2	28	73.7524067558588	876.27549665073
+M74T858	80	73.7524235616046	858.00252803859
+M74T34	345	74.0319853847452	33.6736778224506
+M74T1033	231	74.0963050198453	1033.01869720333
+M75T34	345	74.5303776078914	33.8541677395798
+M75T505	26	74.5552304268754	505.059650753422
+M75T431	1	75.0246219750883	431.003601360729
+M76T1040	89	76.0391694122706	1039.93848585356
+M77T537	50	76.9819350151329	536.652145428441
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_med1_vm.tsv	Thu Mar 11 21:12:46 2021 +0000
@@ -0,0 +1,10 @@
+variableMetadata	sample	trt
+trtA_1	trtA_1	A
+trtA_2	trtA_2	A
+trtA_3	trtA_3	A
+trtB_1	trtB_1	B
+trtB_2	trtB_2	B
+trtB_3	trtB_3	B
+trtC_1	trtC_1	C
+trtC_2	trtC_2	C
+trtC_3	trtC_3	C