changeset 0:caf0ce49b638 draft

planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
author eschen42
date Sun, 18 Jun 2017 23:25:58 -0400
parents
children 17356c5fe43e
files LICENSE README test-data/input_dataMatrix.tsv test-data/input_sampleMetadata.tsv test-data/input_variableMetadata.tsv w4mclstrpeakpics.xml w4mclstrpeakpics_0.98.1.tar.gz w4mclstrpeakpics_wrapper.R
diffstat 8 files changed, 1329 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Hegeman Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,2 @@
+# w4mclstrpeakpics_galaxy_wrapper
+Planemo-based galaxy-tool-wrapper to wrap the w4mclstrpeakpics R package 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_dataMatrix.tsv	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,439 @@
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+M637.4168T982	0	118413.351457918	103078.683730053	63346.5697463526	88691.0687463021	120771.984401155	0	188714.737339463	116855.929076893	0
+M641.1639T235	11186.7696763924	35738.0007249373	0	0	0	0	0	0	0	0
+M641.3852T398	0	832905.756428245	0	0	0	262980.622607653	284941.311105049	290602.100561012	0	201301.66567172
+M641.3779T299	48737.0503941385	115886.494245352	0	0	0	0	155661.316044092	167728.141983407	0	0
+M642.3764T398	0	0	0	0	140746.495442566	0	0	185519.726648991	0	0
+M725.5339T242	0	205786.728339047	0	0	0	0	235153.08541671	0	0	0
+M726.0061T243	133103.702505254	0	288325.504020623	0	0	328213.712775445	0	169283.589882147	56864.2550285423	121351.797212108
+M731.0375T243	83161.9427364442	169316.991230736	218180.79763607	0	0	534641.067170225	0	0	139339.428176695	173579.182616035
+M732.1165T243	0	69371.7983165249	0	0	0	60887.9067902164	0	0	0	0
+M787.437T398	900072.578270501	1172781.66983121	1272978.51379346	1429949.51087332	0	1486628.34634471	1379843.23294773	1345461.30455147	672414.210803648	965068.292144016
+M788.4296T398	554827.169998933	413469.126311578	410619.014740454	518871.525453402	440870.68233934	693241.558960015	0	1047650.28794432	650697.656666683	0
+M789.4071T398	0	0	0	0	227155.719907742	0	0	167916.950822456	122373.599640083	0
+M803.4209T379	0	0	0	0	75539.8209444521	0	0	0	0	74553.1755088707
+M897.0021T280	0	0	0	0	0	0	0	248802.506292246	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_sampleMetadata.tsv	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,11 @@
+sampleMetadata	class	polarity	sampleType	injectionOrder	batch
+pool_RA3_01_211	pool	unknown	pool	211	1
+pool_RA3_01_224	pool	unknown	pool	224	1
+pool_RA3_01_237	pool	unknown	pool	237	1
+pool_RA3_01_250	pool	unknown	pool	250	1
+pool_RA3_01_263	pool	unknown	pool	263	1
+pool_RA3_01_276	pool	unknown	pool	276	1
+pool_RA3_01_289	pool	unknown	pool	289	1
+pool_RA3_01_301	pool	unknown	pool	301	1
+pool_RA3_01_303	pool	unknown	pool	303	1
+pool_RA3_01_310	pool	unknown	pool	310	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_variableMetadata.tsv	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,439 @@
+variableMetadata	mz	mzmin	mzmax	rt	rtmin	rtmax	npeaks	my_blank	pool	y0	y1	y2	y3	y4	y5	y6	y7	y8	y9	isotopes	adduct	pcgroup	CV.samp	CV.pool	CV.ind	blank_mean	blank_sd	blank_CV	sample_mean	sample_sd	sample_CV	blankMean_over_sampleMean	pool_mean	pool_sd	pool_CV	poolCV_over_sampleCV
+M118T229	118	118	118	229.451	228.757	230.425	55	0	8	7	5	7	6	5	2	3	7	3	2			163	1.03349161723371	0.657505675126354	1	0	0	NA	213552.951948849	220705.185674649	1.03349161723371	0	173460.1856975	114051.056504578	0.657505675126354	0.63619836306584
+M143.875T249	143.875	143.875	143.875	248.6925	248.003	249.497	62	0	8	2	7	3	5	7	8	6	5	8	3			200	0.866668428860241	0.590646414075946	1	0	0	NA	289603.268541541	250990.009739687	0.866668428860241	0	249361.796759644	147284.651063619	0.590646414075946	0.681513707442542
+M145.875T229	145.875	145.875	145.875	229.4375	228.757	230.425	62	0	9	8	6	6	6	6	2	6	8	4	1	[2][M]+	[M+H-COCH2]+ 186.873	163	0.86216661133598	0.419645969689113	1	0	0	NA	409771.980931631	353291.720220256	0.86216661133598	0	444322.718560723	186458.238085317	0.419645969689113	0.486734192871196
+M156.875T518	156.875	156.875	156.875	518.478	517.409	519.222	26	0	7	1	0	0	0	0	8	6	1	0	3		[M+H]+ 155.866 [2M+2Na+2K-H]3+ 173.868 [M+H-HCOOH]+ 201.871	109	1.99854477563612	0.787384312150848	1	0	0	NA	529902.224912445	1059033.32319672	1.99854477563612	0	466542.805598216	367348.486074878	0.787384312150848	0.393978819864184
+M161.875T214	161.875	161.875	161.875	214.045	212.89	215.483	33	0	4	5	5	0	3	4	4	2	2	3	1			11687	1.96026178189654	1.38517423954301	1	0	0	NA	110632.822330798	216869.293438413	1.96026178189654	0	58255.7875136068	80694.4161681395	1.38517423954301	0.706627172113138
+M162.875T243	162.875	162.75	162.875	242.9005	242.021	244.244	50	0	4	5	4	5	5	3	7	4	6	5	2	[6][M]+	[M+Na]+ 139.89	27	6.6217595200987	1.24094454281202	1	0	0	NA	35956557.2884005	238095675.53444	6.6217595200987	0	1933778.01020922	2399711.26877902	1.24094454281202	0.187404048583378
+M162.875T227	162.875	162.75	162.875	226.88	225.834	227.841	33	0	3	2	5	3	2	1	1	4	4	5	3			292	2.46582642155519	1.26025006039277	1	0	0	NA	429412.075735207	1058855.64208273	2.46582642155519	0	75717.8626391249	95423.4409637687	1.26025006039277	0.511086283031202
+M164.875T317	164.875	164.875	164.875	317.047	316.063	317.901	53	0	4	0	8	8	8	8	8	6	0	0	3		[M+K]+ 125.917 [M+H-CO2]+ 207.865	99	3.20777891158024	1.22281074457447	1	0	0	NA	1796521.97807089	5762845.31544622	3.20777891158024	0	179368.717678501	219333.995217816	1.22281074457447	0.381201690727519
+M164.875T256	164.875	164.75	164.875	255.82	253.918	256.342	32	0	8	0	2	2	7	5	4	4	0	0	0		[M+H]+ 163.866	161	1.83002344159852	0.609311706957135	1	0	0	NA	261534.09812818	478613.530351897	1.83002344159852	0	334362.764445135	203731.146746972	0.609311706957135	0.332952951916782
+M164.875T338	164.875	164.875	164.875	337.558	336.617	338.134	54	0	7	0	8	8	7	7	7	6	0	0	4			87	2.40774480103077	0.631738765227183	1	0	0	NA	623548.929038994	1501346.69208194	2.40774480103077	0	293469.407076251	185396.000858304	0.631738765227183	0.262377792263006
+M165.875T317	165.875	165.875	165.875	317.039	316.063	317.901	56	0	5	0	8	8	8	8	8	7	0	0	4	[7][M]+		99	1.10982997321072	1.02611672985688	1	0	0	NA	751103.286991909	833596.940880711	1.10982997321072	0	252456.476205591	259049.813795273	1.02611672985688	0.924571109652362
+M165.875T337	165.875	165.75	165.875	337.431	335.212	338.152	53	0	8	0	7	8	7	8	6	5	0	0	4		[M+Na]+ 142.884	87	1.22056555880782	0.661972274955868	1	0	0	NA	374860.198438206	457541.447581538	1.22056555880782	0	316962.531399836	209820.40798652	0.661972274955868	0.542348807222159
+M166.875T625	166.875	166.875	166.875	624.5695	623.5	625.337	26	0	1	1	2	1	6	3	4	5	0	2	1			208	1.90363556510445	2	1	0	0	NA	92851.8449207545	176756.074276711	1.90363556510445	0	14868.786067849	29737.572135698	2	1.05062126210605
+M172.875T452	172.875	172.875	172.875	451.8905	450.74	453.2	22	0	5	3	4	0	1	2	3	2	2	0	0	[8][M]+	[M+H]+ 171.872 [M+H-CO]+ 199.866	1	2.78501690076941	1.12445204061718	1	0	0	NA	598071.01676608	1665637.88955388	2.78501690076941	0	1174438.67568044	1320599.96544861	1.12445204061718	0.403750526722668
+M172.875T433	172.875	172.875	173	433.3265	432.642	433.957	36	0	6	6	5	1	1	2	6	4	4	0	1		[M+H-HCOOH]+ 217.871	3	1.8465365966236	0.901826895928369	1	0	0	NA	1096654.51681186	2025012.69914568	1.8465365966236	0	1321851.7927057	1192081.49909313	0.901826895928369	0.488388314413785
+M176.875T293	176.875	176.75	176.875	292.918	288.591	293.646	29	0	3	0	4	3	1	1	4	3	6	4	0			174	1.78553962669974	1.53297695722039	1	0	0	NA	158239.044223647	282542.083952415	1.78553962669974	0	69726.2256259003	106888.697198455	1.53297695722039	0.858551070106366
+M180.875T317	180.875	180.875	180.875	317.047	316.34	317.901	59	0	8	0	7	8	8	8	8	8	0	0	4	[11][M]+	[M+K]+ 141.91 [M+Na]+ 157.884 [M+H]+ 179.866 [M+H-CO]+ 207.865 [M+H-HCOOH]+ 225.872	99	0.91774703806549	0.591503598630657	1	0	0	NA	1310802.78391237	1202985.37242358	0.91774703806549	0	957822.821689697	566555.645880026	0.591503598630657	0.644517033667013
+M180.875T338	180.875	180.875	180.875	337.595	336.366	338.069	56	0	6	0	8	7	8	8	8	7	0	0	4		[M+H-HCOOH]+ 225.872	87	3.06840889893882	0.804369492744772	1	0	0	NA	1290483.55836223	3959731.23441291	3.06840889893882	0	463371.137180013	372721.606566055	0.804369492744772	0.26214546992839
+M180.875T540	180.875	180.875	180.875	539.6605	538.843	540.758	30	0	4	0	2	6	6	4	6	2	0	0	0		[2M+2Na+2K-H]3+ 209.865	138	1.67273669509929	1.43314729203548	1	0	0	NA	212333.159931487	355177.468203785	1.67273669509929	0	78769.4950992019	112888.288596423	1.43314729203548	0.856768011507282
+M181.875T317	181.875	181.875	181.875	317.0545	316.477	317.96	22	0	1	0	4	2	5	3	5	1	0	0	1	[11][M+1]+		99	5.42909528817463	2.44948974278318	1	0	0	NA	3401583.05179657	18467518.5188434	5.42909528817463	0	8928.03394827843	21869.127579528	2.44948974278318	0.451178255817047
+M182.875T540	182.875	182.875	182.875	539.773	538.953	540.809	31	0	3	0	4	6	5	4	4	3	0	0	2	[13][M]+	[M+Na]+ 159.882 [M+H-CO]+ 209.865	138	1.56338092205028	1.66150754417057	1	0	0	NA	360221.947424743	563164.120307643	1.56338092205028	0	156034.103228504	259251.839662049	1.66150754417057	1.06276565150329
+M184.875T338	184.875	184.875	185	337.601	336.617	338.902	31	0	6	0	5	4	6	3	4	2	0	1	0		[M+H-COCH2]+ 225.872	87	1.96000288322788	0.962211981228455	1	0	0	NA	211151.492059652	413857.533234786	1.96000288322788	0	155583.34524776	149704.158876998	0.962211981228455	0.49092375805275
+M187.875T229	187.875	187.875	187.875	229.443	228.884	230.425	63	0	9	8	5	5	5	6	5	5	8	5	2	[16][M]+	[M+H]+ 186.873	163	0.982986008710717	0.415337478657392	1	0	0	NA	473571.054078531	465513.720289582	0.982986008710717	0	542476.953358509	225311.010037667	0.415337478657392	0.422526338093203
+M190.875T254	190.875	190.75	190.875	254.1245	253.382	256.444	24	0	5	1	3	1	2	2	2	3	2	1	2		[M+H-CH2]+ 203.885 [M+H-H20]+ 207.872	151	2.04109229797588	1.29123418615319	1	0	0	NA	89534.2529787194	182747.674159889	2.04109229797588	0	165320.290804203	213467.211151175	1.29123418615319	0.63261920464532
+M192.875T540	192.875	192.875	192.875	539.799	538.843	540.809	24	0	2	0	2	5	5	3	5	2	0	0	0			138	2.0481816785158	2.03797414170079	1	0	0	NA	136523.337682168	279624.598930442	2.0481816785158	0	22762.2125527268	46388.8005903543	2.03797414170079	0.995016293270232
+M198.875T338	198.875	198.875	198.875	337.6095	336.617	338.069	34	0	4	0	6	2	8	6	5	3	0	0	0		[M+K+HCOOH]+ 113.912 [M+Na+HCOOH]+ 129.883 [3M+2H]2+ 131.915 [M+K+NH3]+ 142.884	87	2.07024093119042	1.32407129628577	1	0	0	NA	427064.754630852	884126.935305583	2.07024093119042	0	222947.99041051	295199.034667151	1.32407129628577	0.639573528055216
+M206.875T228	206.875	206.875	206.875	227.762	226.91	228.594	21	0	2	0	0	0	2	0	7	1	1	8	0			299	3.1571891227243	1.70807003482249	1	0	0	NA	75069.343366297	237008.114326128	3.1571891227243	0	20815.3857835117	35554.1367200864	1.70807003482249	0.541009729993185
+M207.875T219	207.875	207.875	207.875	218.856	217.82	220.603	37	0	6	0	4	0	1	2	6	2	7	8	1	[19][M]+		3904	2.24443496904264	0.952856477406668	1	0	0	NA	802348.419067389	1800818.84911093	2.24443496904264	0	503945.719226214	480187.94282606	0.952856477406668	0.424541806980091
+M208.875T337	208.875	208.875	208.875	337.473	336.366	338.128	26	0	3	0	4	5	7	3	2	1	0	0	1		[M+H-H20]+ 225.872	87	4.80934681142269	1.41266246747602	1	0	0	NA	485629.600465742	2335561.17053239	4.80934681142269	0	51372.1791748055	72571.5493927008	1.41266246747602	0.293732709007551
+M210.875T540	210.875	210.875	210.875	539.695	538.843	540.496	39	0	5	0	4	8	8	3	7	3	0	0	1		[M+H]+ 209.865	138	1.44279679032265	1.14286778437892	1	0	0	NA	559103.834912698	806673.218469128	1.44279679032265	0	315458.162291032	360526.971001798	1.14286778437892	0.792119716403959
+M220.875T389	220.875	220.875	220.875	389.4505	388.616	390.226	54	0	8	0	6	7	6	8	8	7	0	0	4	[25][M]+		4621	2.1274832160322	0.403007196236642	1	0	0	NA	1186791.38787073	2524878.75862653	2.1274832160322	0	709172.990998993	285801.818749258	0.403007196236642	0.189429083717172
+M222.875T302	222.875	222.875	222.875	301.8435	300.995	302.652	78	0	10	3	8	8	8	8	8	8	5	8	4	[28][M]+		51	0.681317502476254	0.0711658834731154	1	0	0	NA	3136657.10029428	2137059.38169691	0.681317502476254	0	3200039.00559685	227733.602981729	0.0711658834731154	0.104453332278215
+M222.875T251	222.875	222.875	222.875	251.04	249.947	251.658	56	0	9	0	6	6	6	7	7	8	3	0	4	[29][M]+		243	1.04302833621569	0.436400016419828	1	0	0	NA	298121.674858957	310949.354517974	1.04302833621569	0	344784.366287429	150463.903109134	0.436400016419828	0.418397085934568
+M222.875T584	222.875	222.875	222.875	584.167	583.222	586.157	53	0	7	0	7	8	7	7	8	7	0	0	2	[30][M]+		17	1.54567644826109	0.915849846168579	1	0	0	NA	1542962.45234165	2384920.72313566	1.54567644826109	0	773593.162792206	708495.179140306	0.915849846168579	0.592523646976004
+M224T687	224	224	224	687.4965	686.943	688.31	30	0	10	3	2	5	0	3	1	2	2	0	2	[31][M]+		7	5.98065881062989	0.156602627935458	1	0	0	NA	2173993.0229446	13001910.5269215	5.98065881062989	0	2651932.23018486	415299.55635369	0.156602627935458	0.0261848456656842
+M223.875T302	223.875	223.875	223.875	301.818	301.055	302.504	29	0	4	0	4	3	2	2	4	6	0	1	3	[28][M+1]+		51	1.9047157291666	1.42675814170762	1	0	0	NA	340529.692922781	648612.262358292	1.9047157291666	0	164175.282147799	234238.420471518	1.42675814170762	0.749066183399396
+M224.875T266	224.875	224.875	224.875	265.98	265.336	266.969	23	0	4	0	0	3	6	3	4	3	0	0	0			67	3.60162700329031	0.971503674313382	1	0	0	NA	201342.53836011	725160.723068788	3.60162700329031	0	103639.641819202	100686.292831877	0.971503674313382	0.269740223911541
+M226.875T338	226.875	226.875	226.875	337.578	336.617	338.288	43	0	6	0	6	6	7	5	7	4	0	0	2	[33][M]+	[M+H]+ 225.872	87	1.34781844146111	0.885442658388359	1	0	0	NA	1033980.85486022	1393618.46429833	1.34781844146111	0	769282.49374388	681155.536312207	0.885442658388359	0.656945053688751
+M226.875T439	226.875	226.875	226.875	439.494	438.897	440.279	21	0	2	0	2	4	4	8	0	1	0	0	0	[34][M]+	[M+H]+ 225.868	125	4.70498518775428	1.83506771806455	1	0	0	NA	1708279.54014747	8037429.93293752	4.70498518775428	0	76739.382148585	140821.962885087	1.83506771806455	0.390026247657634
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mclstrpeakpics.xml	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,283 @@
+<tool id="w4mclstrpeakpics" name="View Cluster_Peaks" version="0.98.1">
+  <description>Visualize sample-cluster peaks</description>
+
+  <requirements>
+    <requirement type="package" version="3.3.1">r-base</requirement>
+    <requirement type="package" version="1.1_4">r-batch</requirement>
+    <requirement type="package" version="1.4.2">r-reshape2</requirement>
+    <requirement type="package" version="0.4_10">r-sqldf</requirement>
+  </requirements>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+
+  <command detect_errors="exit_code"><![CDATA[
+  Rscript $__tool_directory__/w4mclstrpeakpics_wrapper.R
+  data_matrix_path '$dataMatrix_in'
+  variable_metadata_path '$variableMetadata_in'
+  sample_metadata_path '$sampleMetadata_in'
+  sample_selector_column_name '$sampleSelectorColumnName'
+  sample_selector_value '$sampleSelectorValue'
+  output_pdf '$outputFigure'
+  output_tsv '$outputTable'
+  output_rdata '$outputRdata'
+  r_package_archive $__tool_directory__/w4mclstrpeakpics_0.98.1.tar.gz
+  ; echo exit code $?
+  ]]></command>
+
+  <inputs>
+    <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
+    <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
+    <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
+    <param name="sampleSelectorColumnName" label="Selector-column name" type="text" value = "sampleType" help="Name of column containing selector values." />
+    <param name="sampleSelectorValue" label="Selector value" type="text" value = "pool" help="Value to match in sample-selector column." />
+  </inputs>
+  <outputs>
+    <data name="outputTable" label="${tool.name}_${sampleSelectorValue}_table" format="tabular" ></data>
+    <data name="outputFigure" label="${tool.name}_${sampleSelectorValue}_figure" format="pdf" ></data>
+    <data name="outputRdata" label="${tool.name}_${sampleSelectorValue}_RData" format="rdata" ></data>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
+      <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
+      <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
+      <param name="sampleSelectorColumnName" value="sampleType"/>
+      <param name="sampleSelectorValue" value="pool"/>
+	  <output name="outputTable">
+        <assert_contents>
+          <has_text text="0.464572" />
+          <has_text text="0.114304" />
+          <has_text text="0.131016" />
+          <has_text text="0.0701871" />
+          <has_text text="0.0661764" />
+          <has_text text="0.0384358" />
+          <has_text text="0.0614973" />
+          <has_text text="0.0260695" />
+          <has_text text="0.0193850" />
+          <has_text text="0.00835561" />
+        </assert_contents>
+	  </output>
+    </test>
+  </tests>
+
+
+
+	<help>
+		<![CDATA[
+
+**Author**	Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
+
+--------------------------------------------------------------------------
+
+
+**R package**
+
+The *w4mclstrpeakpics* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclstrpeakpics/releases).
+
+-----------------------------------------------------------------------------------------------------------------------------------------
+
+
+**Tool updates**
+
+See the **NEWS** section at the bottom of this page
+
+---------------------------------------------------
+
+==================================
+Visualize W4M sample-cluster peaks
+==================================
+
+-----------
+Description
+-----------
+
+Produce a figure to assess the similarities and differences among peaks in a cluster of samples using XCMS-preprocessed data files as input.
+
+-----------------
+Workflow Position
+-----------------
+
+  - Upstream tool category: Preprocessing
+  - Downstream tool categories: (Not applicable.)
+
+----------
+Motivation
+----------
+
+GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio. 
+Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time.
+Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ. 
+However, the chromatographic retention time for a chemical can vary from one run to another.
+In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples.
+
+In a typical GC-MS or LC-MS experiment, a pooled sample is repeatedly injected for quality control.
+Since this is the same mixture for each injection, the identified peaks would be expected to be identical for all injections.
+However, the parameters for peak-picking can exacerbate injection-to-injection variation in performance of the experimental apparatus.
+This tool exists to assess the variation in the peaks picked among pooled samples, replicates, or indeed any cluster of samples.
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| File                      |   Format   |
++===========================+============+
+|     Data matrix           |   tabular  |
++---------------------------+------------+
+|     Sample metadata       |   tabular  |
++---------------------------+------------+
+|     Variable metadata     |   tabular  |
++---------------------------+------------+
+
+
+----------
+Parameters
+----------
+
+Data matrix file
+	| variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
+	|
+
+Sample metadata file
+	| sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
+	|
+
+Variable metadata file
+	| variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
+	|
+
+Selector-column name (default = "sampleType")
+	| column of W4M/XCMS sampleMetadata holding selector string values.
+	|
+
+Selector value (default = "pool")
+	| value within selector column to identify samples for assessment.
+	|
+
+Include named classes (default = filter-out)
+	| *filter-in* - include only the named sample classes
+	| *filter-out* - exclude only the named sample classes
+	|
+
+
+Column that names the sample-class (default = 'class')
+	| name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
+	|
+
+Column that names the sample (default = 'sampleMetadata')
+	| name of the column in sample metadata that has the name of the sample
+	|
+
+
+------------
+Output files
+------------
+
+
+View Cluster_Peaks_<SelectorName>_figure
+	| (PDF) the output figure, described below.
+	|
+
+View Cluster_Peaks_<SelectorName>_table
+	| (tabular separated values) table of the values plotted in the upper-left graph in the output figure.
+	|
+
+View Cluster_Peaks_<SelectorName>_rdata
+	| (R data) RData containing all processing and plotting intermediates..
+	|
+
+
+------
+Graphs
+------
+
+
+**The "Feature Number and Likelihood" graph**
+
+The upper left graph in the output figure shows the following:
+
+* The X axis reflects the number of samples in which a given feature is present (“the prevalance of a feature among the samples”).
+* For open circles, the Y axis reflects the number of features having the number of samples reflected on the X axis.
+* For solid triangles, the Y axis reflects the relative likelihood of features having the number of samples reflected on the X axis, calculated as
+
+	.. math:: \frac{(number\hspace{1 mm}of\hspace{1 mm}features) (number\hspace{1 mm}of\hspace{1 mm}samples\hspace{1 mm}per\hspace{1 mm}feature)}{maximum(number\hspace{1 mm}of\hspace{1 mm}samples\hspace{1 mm}per\hspace{1 mm}feature)}
+
+Ideally, there would be an upward trend from left to right; if not, XCMS peak-picking parameters may need to be adjusted to suppress low-intensity “noise” peaks or to address peak-splitting.
+
+
+**The "Peak Intensity" graph**
+
+The lower left graph in the output figure presents the data in the upper figure without summarization, so that “the eye” can do the interpretation. It shows the following:
+
+* The X axis reflects the number of samples in which a given feature is present (“the prevalance of a feature among the samples”).
+* The Y axis reflects the intensity each sample for each feature having the number of samples reflected on the X axis.
+
+Ideally, there would be an upward trend from left to right, with more points on the right; if not, XCMS peak-picking parameters may need to be adjusted to suppress low-intensity “noise” peaks or to address peak-splitting.
+
+
+**The "Symbol area/intensity reflect ion intensity" graph**
+
+The upper right graph in the output figure shows the following:
+
+* The X axis reflects the corrected retention time for each feature shown.
+* The Y axis reflects the m/z for each feature shown.
+* Symbol area reflects intensity for a feature for one sample.
+* Overlapping symbols make the overlapping area darker, so the area and darkness reflect the aggregated intensity of a feature. (It is doubtful that a densitometer would be able to recover aggregate intensities accurately from this graph, but philosophically that is how this graph is designed.)
+* The graph is not designed to communicate prevalence of a feature among the samples, but the hue of the symbol reflects the prevalance, albeit subtly.
+
+Consequently, if the graph has a lot of large, dark, blueish symbols for repeated runs of a pooled sample, there is strong evidence that the XCMS peak-picking parameters need adjustment to make peak-picking more consistent.
+
+
+**The "Symbol size/shape reflects prevalence" graph**
+
+By contrast with the area/intensity graph, lower right graph’s primary purpose is to communicate prevalence of a feature among the samples. It`shows the following:
+
+* The X axis reflects the corrected retention time for each feature shown.
+* The Y axis reflects the m/z for each feature shown.
+* Symbol size and shape reflect the prevalence of a feature among the samples.
+* “Vividness” of color reflects the aggregate intensity across all samples for a feature, in an attempt to draw attention to the more intense features.
+
+Consequently, if the graph has a lot of small, vivid symbols for repeated runs of a pooled sample, there is strong evidence that the XCMS peak-picking parameters need adjustment to make peak-picking more consistent.
+
+
+---------------
+Working example
+---------------
+
+**Input files**
+
++-------------------+----------------------------------------------------------------------------------------------------------------+
+| Input File        | Download from URL                                                                                              |
++===================+================================================================================================================+
+| Data matrix       | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_dataMatrix.tsv       |
++-------------------+----------------------------------------------------------------------------------------------------------------+
+| Sample metadata   | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_sampleMetadata.tsv   |
++-------------------+----------------------------------------------------------------------------------------------------------------+
+| Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_variableMetadata.tsv |
++-------------------+----------------------------------------------------------------------------------------------------------------+
+
+**Other input parameters**
+
++------------------------------------+-----------------+
+| Input Parameter                    | Value           |
++====================================+=================+
+| Selector-column name               | sampleType      |
++------------------------------------+-----------------+
+| Selector value                     | pool            |
++------------------------------------+-----------------+
+
+
+
+    ]]>
+  </help>
+  <citations>
+    <citation type="doi">10.1021/ac051437y</citation>
+    <citation type="doi">10.1093/bioinformatics/btu813</citation>
+  </citations>
+  <!--
+     vim:noet:sw=4:ts=4
+--> </tool>
Binary file w4mclstrpeakpics_0.98.1.tar.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mclstrpeakpics_wrapper.R	Sun Jun 18 23:25:58 2017 -0400
@@ -0,0 +1,134 @@
+#!/usr/bin/env Rscript
+
+library(batch) ## parseCommandArgs
+
+########
+# MAIN #
+########
+
+argVc <- unlist(parseCommandArgs(evaluate=FALSE))
+
+##------------------------------
+## Initializing
+##------------------------------
+
+## options
+##--------
+
+strAsFacL <- options()$stringsAsFactors
+options(stringsAsFactors = FALSE)
+
+## libraries
+##----------
+
+# begin HACK - suppress " Can't find a usable init.tcl ...  probably means that Tcl wasn't installed properly" issue
+library("gsubfn")
+options(gsubfn.engine = "R")
+# end HACK
+
+r_package_archive <- as.character(argVc["r_package_archive"])
+install.packages(r_package_archive, repos = NULL, type = "source")
+suppressMessages( library("w4mclstrpeakpics") )
+
+## constants
+##----------
+
+modNamC <- "w4mclsltrpeakpics" ## module name
+
+topEnvC <- environment()
+flgC <- "\n"
+
+## functions
+##----------
+
+
+## log file
+##---------
+
+my_print <- function(x, ...) { cat(c(x, ...))}
+
+my_print("\nStart of the '", modNamC, "' Galaxy module call: ",
+    format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
+
+## arguments
+##----------
+
+# files
+
+output_pdf                  <- as.character(argVc["output_pdf"])
+output_tsv                  <- as.character(argVc["output_tsv"])
+output_rdata                <- as.character(argVc["output_rdata"])
+data_matrix_path            <- as.character(argVc["data_matrix_path"])
+variable_metadata_path      <- as.character(argVc["variable_metadata_path"])
+sample_metadata_path        <- as.character(argVc["sample_metadata_path"])
+  
+# other parameters
+
+sample_selector_column_name <- as.character(argVc["sample_selector_column_name"])
+sample_selector_value       <- as.character(argVc["sample_selector_value"])
+  
+##------------------------------
+## Computation
+##------------------------------
+
+# from 'demo(error.catching)'
+tryCatch.W.E <- function(expr) {
+  W <- NULL
+  w.handler <- function(w){
+    # warning handler
+    W <<- w
+    invokeRestart("muffleWarning")
+  }
+  list(
+    value = withCallingHandlers(
+      tryCatch(expr, error = function(e) e)
+    , warning = w.handler
+    )
+  , warning = W
+  )
+}
+
+result <- cluster_peak_assessment(
+  sample_selector_column_name = sample_selector_column_name
+, sample_selector_value       = sample_selector_value      
+, sample_metadata_path        = sample_metadata_path  
+, variable_metadata_path      = variable_metadata_path
+, data_matrix_path            = data_matrix_path      
+, output_pdf                  = output_pdf            
+, output_tsv                  = output_tsv            
+, output_rdata                = output_rdata                 
+, failure_action              = my_print
+)
+
+
+my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",
+    as.character(result), "\n", sep = "")
+
+##--------
+## Closing
+##--------
+
+my_print("\nEnd of '", modNamC, "' Galaxy module call: ",
+    as.character(Sys.time()), "\n", sep = "")
+
+#sink()
+
+if (!file.exists(output_pdf)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_pdf))
+}
+
+if (!file.exists(output_tsv)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_tsv))
+}
+
+if (!file.exists(output_rdata)) {
+  print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, output_rdata))
+}
+
+# 'stop' causes Rscript to return a non-zero exit code
+if( !result ) {
+  stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
+}
+
+# exit with status code zero
+q(save = "no", status = 0, runLast = FALSE)