# HG changeset patch
# User tomnl
# Date 1528718317 14400
# Node ID bc86834acaedd74bf969ca631d0800fda8636a2c
# Parent  3c6ba952c41b748a9c155510a55a80697b625f17
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 25e4ea47403332a6efd413d13a52511eb4ab5110-dirty

diff -r 3c6ba952c41b -r bc86834acaed create_sqlite_db.R
--- a/create_sqlite_db.R	Sat Jun 02 06:50:56 2018 -0400
+++ b/create_sqlite_db.R	Mon Jun 11 07:58:37 2018 -0400
@@ -7,7 +7,7 @@
 
 
 xset_pa_filename_fix <- function(opt, pa, xset){
-
+  print(xset@filepaths)
 
   if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
     # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables 
@@ -41,6 +41,9 @@
   }
 
 
+print(xset@phenoData)
+print(xset@filepaths)
+
   return(list(pa, xset))
 }
 
@@ -76,6 +79,7 @@
 
 print(paste('pa', opt$pa))
 print(opt$xset)
+
 print(opt$xcms_camera_option)
 # Requires
 pa <- loadRData(opt$pa, 'pa')
@@ -111,8 +115,6 @@
 
 
 
-
-
 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
                           grp_peaklist=grp_peaklist, db_name=opt$db_name)
 
diff -r 3c6ba952c41b -r bc86834acaed create_sqlite_db.xml
--- a/create_sqlite_db.xml	Sat Jun 02 06:50:56 2018 -0400
+++ b/create_sqlite_db.xml	Mon Jun 11 07:58:37 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.19">
+<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.20">
     <description>
         Create SQLite database of an XCMS-CAMERA dataset
     </description>
diff -r 3c6ba952c41b -r bc86834acaed macros.xml
--- a/macros.xml	Sat Jun 02 06:50:56 2018 -0400
+++ b/macros.xml	Mon Jun 11 07:58:37 2018 -0400
@@ -2,7 +2,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-           <requirement type="package" version="1.5.4" >bioconductor-mspurity</requirement>
+           <requirement type="package" version="1.7.2" >bioconductor-mspurity</requirement>
            <requirement type="package" version="1.4.4" >r-optparse</requirement>
             <yield />
         </requirements>
diff -r 3c6ba952c41b -r bc86834acaed test-data/assess_purity_msms_output_LCMSMS1.tsv
--- a/test-data/assess_purity_msms_output_LCMSMS1.tsv	Sat Jun 02 06:50:56 2018 -0400
+++ b/test-data/assess_purity_msms_output_LCMSMS1.tsv	Mon Jun 11 07:58:37 2018 -0400
@@ -1,830 +1,830 @@
-"pid"	"fileid"	"seqNum"	"precursorIntensity"	"precursorMZ"	"precursorRT"	"precursorScanNum"	"id"	"filename"	"precursorNearest"	"seqNum"	"aMz"	"aPurity"	"apkNm"	"iMz"	"iPurity"	"ipkNm"	"inPkNm"	"inPurity"
-1	"1"	7	2338044.25	391.283841833865	2.70701592	6	7	"dataset_9.dat"	6	7	391.283843994141	1	1	391.283843994141	1	1	1	1
-2	"1"	8	1415939.75	149.023234587846	2.70701592	6	8	"dataset_9.dat"	6	8	149.023254394531	0.85356996593666	2	149.023254394531	0.85356996593666	2	2	0.84752404379021
-3	"1"	9	1319700.25	135.101521833482	2.70701592	6	9	"dataset_9.dat"	6	9	135.101531982422	0.761668785396351	4	135.101531982422	0.761668785396351	4	4	0.75587307549212
-4	"1"	10	1179373.875	219.17415532154	2.70701592	6	10	"dataset_9.dat"	12	10	219.174194335938	0.71736356553493	3	219.174194335938	0.71736356553493	3	3	0.724848945860106
-5	"1"	11	1065425.875	136.02	2.70701592	6	11	"dataset_9.dat"	12	11	136.021514892578	0.816352149356296	4	136.021514892578	0.816352149356296	4	3	0.824735461590834
-6	"1"	13	817673.6875	235.169039094573	3.58374588	12	13	"dataset_9.dat"	12	13	235.169082641602	0.831227778572949	2	235.169082641602	0.831227778572949	2	2	0.829936941935826
-7	"1"	14	775331.375	158.153859911664	3.58374588	12	14	"dataset_9.dat"	12	14	158.153884887695	0.829854737314139	2	158.153884887695	0.829854737314139	2	2	0.834760067588775
-8	"1"	15	600708.3125	371.10089096142	3.58374588	12	15	"dataset_9.dat"	12	15	371.100952148438	1	1	371.100952148438	1	1	1	1
-9	"1"	16	714967.3125	171.149077210391	3.58374588	12	16	"dataset_9.dat"	18	16	171.149078369141	0.770605145884943	3	171.149078369141	0.770605145884943	3	3	0.771140699993925
-10	"1"	17	589836.0625	163.132751968058	3.58374588	12	17	"dataset_9.dat"	18	17	163.132751464844	0.703678395528551	5	163.132751464844	0.703678395528551	5	5	0.705767932040045
-11	"1"	19	553794.9375	187.126277455433	4.46113794	18	19	"dataset_9.dat"	18	19	187.126281738281	0.649302153231548	3	187.126281738281	0.649302153231548	3	3	0.653430821467905
-12	"1"	20	492661.1875	279.16	4.46113794	18	20	"dataset_9.dat"	18	20	279.158843994141	0.778623697012972	2	279.158843994141	0.778623697012972	2	2	0.768109636260892
-13	"1"	21	457835	199.169165972297	4.46113794	18	21	"dataset_9.dat"	18	21	199.169189453125	0.640572224559637	5	199.169189453125	0.640572224559637	5	4	0.648700965647493
-14	"1"	22	461488.96875	202.180046526767	4.46113794	18	22	"dataset_9.dat"	24	22	202.180053710938	0.819821135178155	3	202.180053710938	0.819821135178155	3	3	0.823391317774572
-15	"1"	23	410119.71875	195.087600280852	4.46113794	18	23	"dataset_9.dat"	24	23	195.087631225586	0.417733265197226	7	195.087631225586	0.417733265197226	7	7	0.421824063810413
-16	"1"	25	402203.90625	114.091586894802	5.33426184	24	25	"dataset_9.dat"	24	25	114.091598510742	0.926372857972172	2	114.091598510742	0.926372857972172	2	2	0.925055527958708
-17	"1"	26	323160.375	200.02	5.33426184	24	26	"dataset_9.dat"	24	26	200.02294921875	0.729113582408091	5	200.02294921875	0.729113582408091	5	5	0.726672249502491
-18	"1"	27	396180	195.02	5.33426184	24	27	"dataset_9.dat"	24	27	195.087631225586	0.417733265197226	7	195.087631225586	0.417733265197226	7	7	0.424821037634938
-19	"1"	28	327420.75	329	5.33426184	24	28	"dataset_9.dat"	30	28	329.004913330078	1	1	329.004913330078	1	1	1	1
-20	"1"	29	324730.3125	209.153514427722	5.33426184	24	29	"dataset_9.dat"	30	29	209.153472900391	0.695619209305788	4	209.153472900391	0.695619209305788	4	4	0.693557888944958
-21	"1"	31	339743.09375	327.01	6.2921406	30	31	"dataset_9.dat"	30	31	327.0078125	1	1	327.0078125	1	1	1	1
-22	"1"	32	335606.21875	136.94	6.2921406	30	32	"dataset_9.dat"	30	32	136.940093994141	0.531332725634933	6	136.940093994141	0.531332725634933	6	6	0.542886179140372
-23	"1"	33	333958.6875	197.15	6.2921406	30	33	"dataset_9.dat"	30	33	197.153518676758	0.763123214238007	4	197.153518676758	0.763123214238007	4	5	0.751421175411059
-24	"1"	34	291105.25	116.99	6.2921406	30	34	"dataset_9.dat"	36	34	116.986083984375	0.701600180224725	4	116.986083984375	0.701600180224725	4	5	0.700442939564303
-25	"1"	35	286836.375	202.97	6.2921406	30	35	"dataset_9.dat"	36	35	202.969161987305	0.628338026743662	5	202.969161987305	0.628338026743662	5	5	0.625329369631148
-26	"1"	37	290515.53125	151.11	7.1622666	36	37	"dataset_9.dat"	36	37	151.111679077148	0.644347814959557	5	151.111679077148	0.644347814959557	5	7	0.633773056396492
-27	"1"	38	285627.625	161.1	7.1622666	36	38	"dataset_9.dat"	36	38	161.095993041992	0.467002568844987	7	161.095993041992	0.467002568844987	7	7	0.495775785847218
-28	"1"	39	1468082.875	149.01	7.1622666	36	39	"dataset_9.dat"	36	39	149.023284912109	0.823365295855268	3	149.023284912109	0.823365295855268	3	2	0.869059803274988
-29	"1"	40	531139.375	187	7.1622666	36	40	"dataset_9.dat"	42	40	186.995376586914	0.227279890557788	6	187.126358032227	0.702898652929221	3	3	0.678721150138633
-30	"1"	41	271666.53125	262.981592499906	7.1622666	36	41	"dataset_9.dat"	42	41	262.981658935547	1	1	262.981658935547	1	1	1	1
-31	"1"	43	1002266.8125	219.02	8.0398962	42	43	"dataset_9.dat"	42	43	219.174301147461	0.873278430512564	3	219.174301147461	0.873278430512564	3	3	0.853081454029767
-32	"1"	44	134474.40625	143.106611864554	8.0398962	42	44	"dataset_9.dat"	42	44	143.106674194336	0.833249204699096	2	143.106674194336	0.833249204699096	2	2	0.827834215345055
-33	"1"	45	180732.953125	170.1	8.0398962	42	45	"dataset_9.dat"	42	45	170.096405029297	0.891823182693097	2	170.096405029297	0.891823182693097	2	4	0.844541500699627
-34	"1"	46	151208.578125	132.101942587764	8.0398962	42	46	"dataset_9.dat"	48	46	132.101959228516	0.941783359267288	2	132.101959228516	0.941783359267288	2	2	0.938959916868783
-35	"1"	47	221487.78125	419.315378713978	8.0398962	42	47	"dataset_9.dat"	48	47	419.315307617188	1	1	419.315307617188	1	1	1	1
-36	"1"	49	241524.0625	429.240051060079	8.9065098	48	49	"dataset_9.dat"	48	49	429.239990234375	0.938739677984808	2	429.239990234375	0.938739677984808	2	1	0.948949731654007
-37	"1"	50	259990.203125	175.12	8.9065098	48	50	"dataset_9.dat"	48	50	175.118911743164	0.425736454432608	7	175.118911743164	0.425736454432608	7	8	0.409630706752312
-38	"1"	51	249161.15625	115.08	8.9065098	48	51	"dataset_9.dat"	48	51	115.075614929199	0.657641778785045	7	115.075614929199	0.657641778785045	7	6	0.652670708422347
-39	"1"	52	249687.59375	193.06	8.9065098	48	52	"dataset_9.dat"	54	52	193.055709838867	0.529797352360269	6	193.055709838867	0.529797352360269	6	6	0.538878787850543
-40	"1"	53	247540.765625	104.99	8.9065098	48	53	"dataset_9.dat"	54	53	104.992637634277	0.836210207270544	3	104.992637634277	0.836210207270544	3	3	0.834563123014501
-41	"1"	55	219777.515625	226.162035817238	9.7693968	54	55	"dataset_9.dat"	54	55	226.162002563477	0.901700542299619	3	226.162002563477	0.901700542299619	3	2	0.909577208864804
-42	"1"	56	236618.3125	191.02	9.7693968	54	56	"dataset_9.dat"	54	56	191.022613525391	0.517729753772271	7	191.022613525391	0.517729753772271	7	7	0.5387170942027
-43	"1"	57	212668.125	157.12	9.7693968	54	57	"dataset_9.dat"	54	57	157.122283935547	0.690388392546007	3	157.122283935547	0.690388392546007	3	3	0.714015151278833
-44	"1"	58	218863.296875	169.12	9.7693968	54	58	"dataset_9.dat"	60	58	169.12223815918	0.626059207115619	5	169.12223815918	0.626059207115619	5	6	0.621503239652088
-45	"1"	59	211104.46875	153.127310725365	9.7693968	54	59	"dataset_9.dat"	60	59	153.127319335938	0.523411379317455	4	153.127319335938	0.523411379317455	4	4	0.522191968083064
-46	"1"	61	217535.640625	218.14	10.651878	60	61	"dataset_9.dat"	60	61	218.138595581055	0.613660219740867	6	218.138595581055	0.613660219740867	6	6	0.604339227179466
-47	"1"	62	1172288.125	218.94	10.651878	60	62	"dataset_9.dat"	60	62	219.174209594727	0.716118864305864	3	219.174209594727	0.716118864305864	3	3	0.720092245335111
-48	"1"	63	182002.4375	249.184704613906	10.651878	60	63	"dataset_9.dat"	60	63	249.184707641602	1	1	249.184707641602	1	1	1	1
-49	"1"	64	192958.5625	141.09	10.651878	60	64	"dataset_9.dat"	66	64	141.090896606445	0.717278756734214	5	141.090896606445	0.717278756734214	5	4	0.729146583359962
-50	"1"	65	186895.328125	214.089523515856	10.651878	60	65	"dataset_9.dat"	66	65	214.089477539062	0.771662458733845	4	214.089477539062	0.771662458733845	4	4	0.774411698032456
-51	"1"	67	2217833.25	391.283923908062	11.5240128	66	67	"dataset_9.dat"	66	67	391.283874511719	1	1	391.283874511719	1	1	1	1
-52	"1"	68	1358709	149.023301185453	11.5240128	66	68	"dataset_9.dat"	66	68	149.02326965332	0.834255839372277	2	149.02326965332	0.834255839372277	2	2	0.834510504991426
-53	"1"	69	1233880.5	135.101575187643	11.5240128	66	69	"dataset_9.dat"	66	69	135.101547241211	0.736948037952487	4	135.101547241211	0.736948037952487	4	4	0.740524349412436
-54	"1"	70	1211479.25	219.174175272093	11.5240128	66	70	"dataset_9.dat"	72	70	219.174194335938	0.707403012246031	3	219.174194335938	0.707403012246031	3	3	0.714281677295222
-55	"1"	71	175975.71875	133.03	11.5240128	66	71	"dataset_9.dat"	72	71	133.034606933594	0.584981780977403	6	133.034606933594	0.584981780977403	6	6	0.584136998061953
-56	"1"	73	989788.3125	136.02	12.4006308	72	73	"dataset_9.dat"	72	73	136.021514892578	0.865662146702859	3	136.021514892578	0.865662146702859	3	3	0.863298107064044
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-58	"1"	75	828187.5625	158.153874128027	12.4006308	72	75	"dataset_9.dat"	72	75	158.153884887695	0.844026282776459	2	158.153884887695	0.844026282776459	2	2	0.836793008876384
-59	"1"	76	648126.3125	371.100928734859	12.4006308	72	76	"dataset_9.dat"	78	76	371.101013183594	1	1	371.101013183594	1	1	1	1
-60	"1"	77	630386.3125	171.149075604951	12.4006308	72	77	"dataset_9.dat"	78	77	171.14909362793	0.785879158138024	3	171.14909362793	0.785879158138024	3	3	0.780340087711715
-61	"1"	79	547537.3125	163.132748845233	13.2763908	78	79	"dataset_9.dat"	78	79	163.132766723633	0.684213917555967	5	163.132766723633	0.684213917555967	5	5	0.687680373552428
-62	"1"	80	463423.78125	279.16	13.2763908	78	80	"dataset_9.dat"	78	80	279.158874511719	0.733368262081629	2	279.158874511719	0.733368262081629	2	2	0.748235101742531
-63	"1"	81	498574.1875	187.126267370818	13.2763908	78	81	"dataset_9.dat"	78	81	187.126281738281	0.650525837036721	3	187.126281738281	0.650525837036721	3	3	0.640562003851888
-64	"1"	82	469941.65625	202.180057235494	13.2763908	78	82	"dataset_9.dat"	84	82	202.180038452148	0.81913006937147	3	202.180038452148	0.81913006937147	3	3	0.821819844072031
-65	"1"	83	436781.4375	199.169180050461	13.2763908	78	83	"dataset_9.dat"	84	83	199.169174194336	0.608014887028147	6	199.169174194336	0.608014887028147	6	5	0.610456718376517
-66	"1"	85	402306.90625	114.091591130324	14.15301	84	85	"dataset_9.dat"	84	85	114.091590881348	0.920924423111855	2	114.091590881348	0.920924423111855	2	2	0.92074473419371
-67	"1"	86	395351.875	195.087605026366	14.15301	84	86	"dataset_9.dat"	84	86	195.087615966797	0.41894156721595	7	195.087615966797	0.41894156721595	7	7	0.424307755006033
-68	"1"	87	368317.34375	200.02	14.15301	84	87	"dataset_9.dat"	84	87	200.022933959961	0.755155870465593	5	200.022933959961	0.755155870465593	5	4	0.775521244071894
-69	"1"	88	395351.875	195.02	14.15301	84	88	"dataset_9.dat"	90	88	195.017532348633	0.332835251465758	7	195.087554931641	0.435040130586201	7	7	0.429673942796117
-70	"1"	89	183151.59375	129.091089410679	14.15301	84	89	"dataset_9.dat"	90	89	129.091018676758	0.421943494364779	7	129.091018676758	0.421943494364779	7	8	0.420978557942509
-71	"1"	91	301197.03125	327.01	15.032397	90	91	"dataset_9.dat"	90	91	327.007781982422	1	1	327.007781982422	1	1	1	1
-72	"1"	92	315184.40625	136.94	15.032397	90	92	"dataset_9.dat"	90	92	136.940048217773	0.552076469663756	6	136.940048217773	0.552076469663756	6	7	0.548326574691124
-73	"1"	93	317340.53125	209.153498878572	15.032397	90	93	"dataset_9.dat"	90	93	209.153427124023	0.671932619792626	4	209.153427124023	0.671932619792626	4	4	0.664278279903673
-74	"1"	94	313051.4375	197.15	15.032397	90	94	"dataset_9.dat"	96	94	197.153518676758	0.733889916185971	4	197.153518676758	0.733889916185971	4	4	0.746659509704147
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+802	"1"	968	968	871154	331.2	130.304688	966	968	"dataset_9.dat"	966	968	331.196929931641	0.888685926529996	2	331.196929931641	0.888685926529996	2	2	0.88960573443862
+803	"1"	969	969	781039.4375	158.153673023859	130.304688	966	969	"dataset_9.dat"	966	969	158.153701782227	0.791171635773301	4	158.153701782227	0.791171635773301	4	3	0.806738874570746
+804	"1"	970	970	32764134	269.13	130.304688	966	970	"dataset_9.dat"	972	970	269.12548828125	0.141370053054037	3	269.087615966797	0.813617514939145	3	3	0.829650086646885
+805	"1"	971	971	155505.515625	229.05	130.304688	966	971	"dataset_9.dat"	972	971	229.047210693359	0.342181004056544	4	229.154266357422	0.50685217799906	4	5	0.507238843865549
+806	"1"	973	973	845536.6875	327.140534136341	131.148558	972	973	"dataset_9.dat"	972	973	327.140594482422	0.727993884858406	2	327.140594482422	0.727993884858406	2	3	0.704180375416617
+807	"1"	974	974	5866483	318.201775150359	131.148558	972	974	"dataset_9.dat"	972	974	318.201873779297	1	1	318.201873779297	1	1	1	1
+808	"1"	975	975	845092.0625	536.25	131.148558	972	975	"dataset_9.dat"	972	975	NA	0	NA	NA	0	NA	NA	0
+809	"1"	976	976	614545.375	345.21	131.148558	972	976	"dataset_9.dat"	978	976	345.212768554688	1	1	345.212768554688	1	1	2	0.976986759297886
+810	"1"	977	977	469308.46875	289.22	131.148558	972	977	"dataset_9.dat"	978	977	289.222900390625	1	1	289.222900390625	1	1	1	1
+811	"1"	979	979	347938.1875	324.1314685619	131.936568	978	979	"dataset_9.dat"	978	979	324.131439208984	1	1	324.131439208984	1	1	1	1
+812	"1"	980	980	38274372	137.045632108302	131.936568	978	980	"dataset_9.dat"	978	980	137.045623779297	1	1	137.045623779297	1	1	1	1
+813	"1"	981	981	2197110.5	537.168354555235	131.936568	978	981	"dataset_9.dat"	978	981	NA	0	NA	NA	0	NA	NA	0
+814	"1"	982	982	6986065	241.154271494938	131.936568	978	982	"dataset_9.dat"	984	982	241.154266357422	1	1	241.154266357422	1	1	1	1
+815	"1"	983	983	202176	409.17	131.936568	978	983	"dataset_9.dat"	984	983	409.170837402344	0.871738208530276	2	409.170837402344	0.871738208530276	2	2	0.884648151922212
+816	"1"	985	985	3128515	215.138771219374	132.71007	984	985	"dataset_9.dat"	984	985	215.138793945312	1	1	215.138793945312	1	1	1	1
+817	"1"	986	986	3218578.75	334.19670553683	132.71007	984	986	"dataset_9.dat"	984	986	334.196746826172	0.926246562183373	2	334.196746826172	0.926246562183373	2	1	0.950831041455582
+818	"1"	987	987	2338164	391.283610514295	132.71007	984	987	"dataset_9.dat"	984	987	391.283660888672	1	1	391.283660888672	1	1	1	1
+819	"1"	988	988	2184468.25	290.17	132.71007	984	988	"dataset_9.dat"	990	988	290.170593261719	1	1	290.170593261719	1	1	1	1
+820	"1"	989	989	1960551.25	356.157702076678	132.71007	984	989	"dataset_9.dat"	990	989	356.157745361328	0.738759984327311	3	356.157745361328	0.738759984327311	3	3	0.735813941108667
+821	"1"	991	991	2031393.5	304.186232352971	133.503804	990	991	"dataset_9.dat"	990	991	304.186279296875	0.909007498607307	2	304.186279296875	0.909007498607307	2	2	0.911376543536852
+822	"1"	992	992	1841302.125	340.183823206705	133.503804	990	992	"dataset_9.dat"	990	992	340.183868408203	0.921859692577257	2	340.183868408203	0.921859692577257	2	2	0.929077630476246
+823	"1"	993	993	1325456.625	389.2	133.503804	990	993	"dataset_9.dat"	990	993	389.202545166016	1	1	389.202545166016	1	1	1	1
+824	"1"	994	994	1091136.25	342.14	133.503804	990	994	"dataset_9.dat"	996	994	342.142120361328	1	1	342.142120361328	1	1	1	1
+825	"1"	995	995	997170.5625	483.314830443476	133.503804	990	995	"dataset_9.dat"	996	995	483.31494140625	0.706612336062495	3	483.31494140625	0.706612336062495	3	3	0.711714458623578
+826	"1"	997	997	3670711.25	269.16	134.305698	996	997	"dataset_9.dat"	996	997	269.087707519531	0.504195818495762	3	269.087707519531	0.504195818495762	3	3	0.504195818495762
+827	"1"	998	998	96664.6484375	575.124300805729	134.305698	996	998	"dataset_9.dat"	996	998	NA	0	NA	NA	0	NA	NA	0
+828	"1"	999	999	71747.3984375	118.08638548293	134.305698	996	999	"dataset_9.dat"	996	999	118.086380004883	1	1	118.086380004883	1	1	1	1
+829	"1"	1000	1000	1000603.0625	359.228373720717	134.305698	996	1000	"dataset_9.dat"	996	1000	359.228363037109	0.929710258388609	2	359.228363037109	0.929710258388609	2	2	0.929710258388609
diff -r 3c6ba952c41b -r bc86834acaed test-data/curl_out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/curl_out.txt	Mon Jun 11 07:58:37 2018 -0400
@@ -0,0 +1,290 @@
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+    
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+    
+    <script>
+    function extless(input) {
+        return input.replace(/(.*)\.[^.]+$/, '$1');
+    }
+    var require = {
+        shim: {
+            'jquery': [],
+            'jquery.inview': ["jquery"],
+            'jquery.payment': ["jquery"],
+            'jquery.flot': ["jquery"],
+            'jquery.unveil': ["jquery"],
+            'stripe': {
+              exports: 'Stripe'
+            }
+        },
+        paths: {
+            "jquery": extless("/s/js/lib/jquery/dist/jquery.min.87e69028f78d.js"),
+            "jquery.inview": extless("/s/js/lib/jquery.inview/jquery.inview.min.4edba1c65592.js"),
+            "jquery.payment": extless("/s/js/lib/jquery.payment/lib/jquery.payment.e99c05ca79ae.js"),
+            "jquery.unveil": extless("/s/js/lib/unveil/jquery.unveil.min.ac79eb277093.js"),
+            "jquery.flot": extless("/s/js/lib/jquery-flot/jquery.flot.min.9964206e9d7f.js"),
+            "clipboard": extless("/s/js/lib/clipboard/dist/clipboard.min.bd70fd596a23.js"),
+            "mod/floating-warning": extless("/s/js/mod/floating-warning.a21b2abd2884.js"),
+            "mod/list-collapsing": extless("/s/js/mod/list-collapsing.c1a08d3ef9e9.js"),
+            "mod/list-feature": extless("/s/js/mod/list-feature.73529480f25b.js"),
+            "mod/mobile-menu": extless("/s/js/mod/mobile-menu.841726ee903a.js"),
+            "mod/version-switcher": extless("/s/js/mod/version-switcher.c28bb83972bb.js"),
+            "mod/search-key": extless("/s/js/mod/search-key.f3c0a6fcfedd.js"),
+            "mod/stripe-custom-checkout": extless("/s/js/mod/stripe-custom-checkout.aac1352045b7.js"),
+            "mod/stripe-change-card": extless("/s/js/mod/stripe-change-card.682c710317a8.js"),
+            "mod/console-tabs": extless("/s/js/mod/console-tabs.70ce882faaf3.js"),
+            "stripe-checkout": "https://checkout.stripe.com/checkout",
+            "stripe": "https://js.stripe.com/v2/?"  // ? needed due to require.js
+        }
+    };
+    </script>
+    <script data-main="/s/js/main.c16237f43ba2.js" src="/s/js/lib/require.177879fbe7dd.js"></script>
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diff -r 3c6ba952c41b -r bc86834acaed test-data/frag4feature_output.tsv
--- a/test-data/frag4feature_output.tsv	Sat Jun 02 06:50:56 2018 -0400
+++ b/test-data/frag4feature_output.tsv	Mon Jun 11 07:58:37 2018 -0400
@@ -1,324 +1,324 @@
-"grpid"	"mz"	"mzmin"	"mzmax"	"rt"	"rtmin"	"rtmax"	"into"	"intf"	"maxo"	"maxf"	"i"	"sn"	"sample"	"cid"	"filename"	"precurMtchID"	"precurMtchRT"	"precurMtchMZ"	"precurMtchPPM"	"inPurity"	"pid"
-"12"	112.050766766484	112.050651550293	112.087196350098	67.47903	55.2769038	80.361672	36223791.266206	133522503.549415	7158012.5	8555976.39592391	1	21.054952458659	1	9	"dataset_28.dat"	466	64.427298	112.050704956055	0.55162878935702	1	384
-"12"	112.05085569128	112.050621032715	112.120460510254	67.634034	55.4140188	80.555406	36139265.8017591	133395720.51942	7426335.5	8522973.08164079	1	20.3803986860233	2	400	"dataset_27.dat"	472	65.376156	112.050743103027	1.00479600749392	1	1218
-"14"	113.035371704924	113.034713745117	113.059936523438	83.64567	72.171048	96.141564	92812020.095242	366177037.564437	20943314	23904502.6814248	1	27.9839052693883	2	402	"dataset_27.dat"	596	81.344292	113.034736633301	5.61834418239318	1	1321
-"14"	113.03541992282	113.034698486328	113.059997558594	83.441172	72.006432	95.851296	88462324.9597518	348004137.88132	18599380	22772249.3980656	1	27.431622141047	1	11	"dataset_28.dat"	604	81.93093	113.034736633301	6.04491512630164	1	499
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