# HG changeset patch
# User melpetera
# Date 1576579651 0
# Node ID 573520b2e3b0b316ae4c886f63dc60a2f9c3c1d5
# Parent  bcf48aff1077f1a3122b944179c5d673c574e159
Uploaded

diff -r bcf48aff1077 -r 573520b2e3b0 ACF/analytic_correlation_filtration.xml
--- a/ACF/analytic_correlation_filtration.xml	Wed Oct 30 10:50:07 2019 -0400
+++ b/ACF/analytic_correlation_filtration.xml	Tue Dec 17 10:47:31 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="Analytic_correlation_filtration" name="Analytic correlation filtration" version="2019-06-20">
+<tool id="Analytic_correlation_filtration" name="Analytic correlation filtration" version="2019-10-31">
 	<description>
 		: Detect analytic correlation among data and remove them.
 	</description>
@@ -19,6 +19,7 @@
 		#else:
 			#if str($mass_file.liste.mass_list)=="true":
 				#if str($rt_cond.rt_choice)=="true":
+				#if str($rt_cond.rt_choice)=="true":
 					perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m "$mass_file.liste.mass_file_in" -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in"  -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" 
 				#end if
 				#if str($rt_cond.rt_choice)=="false":
@@ -26,10 +27,20 @@
 				#end if
 			#else
 					#if str($rt_cond.rt_choice)=="true":
-						perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list.csv -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" 
+						#if str($method_opt.method_selection)=="LC":
+							perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_LC.csv -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" 
+						#end if
+						#if str($method_opt.method_selection)=="GC":
+							perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_LC_GC.csv -o 2 -d "$dataMatrix_in" -v "$variableMetadata_in" -rt "$rt_cond.rt_threshold" -mass "$mass_file.mass_threshold" 
+						#end if
 					#end if
 					#if str($rt_cond.rt_choice)=="false":
-						perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list.csv -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" 
+						#if str($method_opt.method_selection)=="LC":
+							perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_LC.csv -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" 
+						#end if
+						#if str($method_opt.method_selection)=="GC":
+							perl $__tool_directory__/Analytic_correlation_filtration.pl -f "$file_in" -m $__tool_directory__/data/default_list_GC.csv -o 3 -d "$dataMatrix_in" -v "$variableMetadata_in" -mass "$mass_file.mass_threshold" 
+						#end if
 					#end if
 			#end if
 		#end if
@@ -59,7 +70,12 @@
 					<conditional name="liste">
 						<param name="mass_list" checked="true" falsevalue="false" help="'YES' if you have your own list to upload; 'NO' if you want to use a default list" label="Do you have your own list of mass differences or do you want to use a default list ?" truevalue="true" type="boolean"/>
 						<when value="false">
-						
+							<conditional name="method_opt">
+								<param name="method_selection" label="Are you analysing LC/MS or GC/MS data ?" type="select" display="radio" help="">
+									<option value="LC">LC/MS</option>
+									<option value="GC">GC/MS</option>
+								</param>
+							</conditional>
 						</when>
 						<when value="true">
 							<param type="data" name="mass_file_in" format="tabular,csv" help="The file containing all your report and known mass differences (cf help for file example) " label="Mass differences table (format: tabular or csv) " />
diff -r bcf48aff1077 -r 573520b2e3b0 ACF/data/default_list.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ACF/data/default_list.tabular	Tue Dec 17 10:47:31 2019 +0000
@@ -0,0 +1,225 @@
+adduit	-2H+Na+K	59.9378259
+adduit	H	1.007825032
+adduit	-H+K	37.95588165
+adduit	-H+Na	21.98194425
+adduit	-3H+3Na	65.94583274
+adduit	-4H+4K	151.8235266
+adduit	-4H+4Na	87.92777699
+adduit	-3H+3K	113.8676449
+adduit	-2H+2K	75.9117633
+adduit	-2H+2Na	43.9638885
+adduit	2H 	2.015650064
+adduit	Cl 	34.96885268
+adduit	-2H+Ca 	37.94694092
+isotope	13C db 	0.501677419
+isotope	13C	1.003354838
+isotope	15N	0.997034893
+isotope	18O	2.00424638
+isotope	34S	1.9957959
+isotope	41K	1.99811908
+isotope	37Cl	1.99704991
+isotope	13C2	2.006709676
+isotope	13C3	3.010064513
+isotope	13C+37Cl	3.000404748
+isotope	13C+18O	3.007601218
+isotope	13C+34S	2.999150738
+isotope	44Ca	3.99289082
+adduit	CH3OH	32.02621475
+adduit	CH3CN	41.0265491
+adduit	H2O	18.01056468
+adduit	2(H2O	36.02112937
+adduit	NaCl 	57.95862196
+adduit	HCOOH	46.0054793
+adduit	+(HCOOH)+(HCOOK)	129.9668403
+adduit	+(HCOOH)+(HCOONa)	113.9929029
+adduit	+(HCOOH)+2(HCOONa)	181.9803264
+adduit	HCOOK	83.96136095
+adduit	+(HCOOK)+(HCOONa)	151.9487845
+adduit	HCOONa	67.98742355
+adduit	2(HCOOH)	92.01095861
+adduit	+2(HCOOH)+(HCOOK)	175.9723196
+adduit	+2(HCOOH)+(HCOONa)	159.9983822
+adduit	2(HCOOK)	167.9227219
+adduit	2(HCOONa)	135.9748471
+fragment	C11H18O9	294.0950822
+fragment	C12H16O12	352.064176
+fragment	C12H20O9	308.1107322
+fragment	C2H2O	42.01056468
+fragment	C2H3.	27.0229265
+fragment	C2H3N	41.0265491
+fragment	C2H3NO3	89.01129296
+fragment	C2H3O.	43.01784112
+fragment	C2H4	28.03130013
+fragment	C2H4N.	42.03382553
+fragment	C2H4O	44.02621475
+fragment	C2H5.	29.03857656
+fragment	C2H5N	43.04219916
+fragment	C2H5NO2	75.0320284
+fragment	C2H5O.	45.03349118
+fragment	C2H5O6P	155.9823745
+fragment	C2H6	30.04695019
+fragment	C2H7N	45.05784922
+fragment	C2HNO2	71.00072827
+fragment	C3H4O3	88.01604399
+fragment	C3H5.	41.03857656
+fragment	C3H5NO2	87.0320284
+fragment	-(C3H5O2NS)-(NH3)	136.0306485
+fragment	C3H5O2NS	119.0040994
+fragment	C3H6	42.04695019
+fragment	C3H6O3	90.03169405
+fragment	C3H7.	43.05422662
+fragment	C3H7O2N	89.04767846
+fragment	C3H7O2NS	121.0197495
+fragment	C3H7O6P	169.9980246
+fragment	C4H6	54.04695019
+fragment	C4H6O2	86.03677943
+fragment	C4H6O4	118.0266087
+fragment	C4H7.	55.05422662
+fragment	C4H8O3	104.0473441
+fragment	C4H9	57.07042529
+fragment	C5H7O3N	129.0425931
+fragment	C5H8O3NS	162.0224891
+fragment	C5H8O4	132.0422587
+fragment	C6H10O4	146.0579088
+fragment	-(C6H10O5)-(H2O)	180.0633881
+fragment	C6H10O5	162.0528234
+fragment	C6H10O7	194.0426527
+fragment	C6H8O6	176.032088
+fragment	CH2O	30.01056468
+fragment	-(CH2S)-(HCOOH)	91.99320037
+fragment	-(CH2S)-(NH3)	63.01427016
+fragment	CH2S	45.98772106
+fragment	CH3.	15.0229265
+fragment	CH3COO.	59.01275574
+fragment	CH3COOH	60.02112937
+fragment	CH3N	29.0265491
+fragment	CH3O.	31.01784112
+fragment	CH3OH	32.02621475
+fragment	CH4	16.03130013
+fragment	CH4N.	30.03382553
+fragment	-(CH4S)-(HCOOH)	94.00885043
+fragment	-(CH4S)-(NH3)	65.02992022
+fragment	CH4S	48.00337113
+fragment	CH5N	31.04219916
+fragment	Cl.	34.96830408
+fragment	CO	27.99491462
+fragment	-(CO2)-(CO)	71.98474386
+fragment	CO2	43.98982924
+fragment	-(H2)-(NH3)	19.04219916
+fragment	H2	2.015650064
+fragment	-(H2O)-(CO2)	62.00039392
+fragment	-(H2O)-(HCOOH)	64.01604399
+fragment	-(H2O)-(NH3)	35.03711378
+fragment	H2O	18.01056468
+fragment	-(H2O)-2(CO2)	105.9902232
+fragment	-(H2S)-(H2O)	51.99828575
+fragment	H2S	33.98772106
+fragment	H2SO4	97.96737954
+fragment	H3PO4	97.97689521
+fragment	HCl	35.97667771
+fragment	HCN	27.01089903
+fragment	-(HCOOH)-(HCN)	73.01637834
+fragment	HCOOH	46.0054793
+fragment	HS.	32.97934743
+fragment	-(NC3H9)-(CH3COOH)	119.0946287
+fragment	-(NC3H9)-(H2O)	77.08406397
+fragment	-(NC3H9)-(HCOOH)	105.0789786
+fragment	NC3H9	59.07349929
+fragment	NaCl	57.95862196
+fragment	NH2CO.	44.01309008
+fragment	-(NH3)-(CO2)-(H2O)	79.02694302
+fragment	-(NH3)-(CO2)	61.01637834
+fragment	-(NH3)-(CONH)	60.03236275
+fragment	-(NH3)-(HCOOH)	63.0320284
+fragment	NH3	17.0265491
+fragment	NH3CO	45.02146372
+fragment	NHCO	43.00581365
+fragment	OH.	17.00219105
+fragment	PO3	78.95850549
+fragment	SO2	63.96190024
+fragment	SO3	79.95681486
+fragment	-2(H2O)-(CO2)	80.01095861
+fragment	-2(H2O)-(HCOOH)-(NH3)	99.05315777
+fragment	-2(H2O)-(HCOOH)	82.02660867
+fragment	2(H2O)	36.02112937
+fragment	2(HCOOH)	92.01095861
+fragment	-2(NH3)-(CO)-(CO2)	106.0378421
+fragment	-2(NH3)-(CO)	62.04801281
+fragment	2(NH3)	34.05309819
+fragment	3(H2O)	54.03169405
+fragment	3(NH3)	51.07964729
+fragment	4(H2O)	72.04225874
+fragment	C10H11O3N5	249.0861892
+fragment	C10H13O4N5	267.0967539
+fragment	C10H14O7N5P	347.0630844
+fragment	C10H15O5N5	285.1073186
+fragment	C2H3NO2	73.01637834
+fragment	C2H4O2	60.02112937
+fragment	C2H5NO3	91.02694302
+fragment	C2H6O2	62.03677943
+fragment	C2H6O3	78.03169405
+fragment	-(C2H6O3)-(H2O)	96.04225874
+fragment	C2H6O4	94.02660867
+fragment	C2H7NO2	77.04767846
+fragment	C3H10O5	126.0528234
+fragment	-(C3H6O3)-(CHNO)	133.0375077
+fragment	C3H6O4	106.0266087
+fragment	C3H8O3	92.04734412
+fragment	C3H8O4	108.0422587
+fragment	C4H10O5	138.0528234
+fragment	C4H5NO3	115.026943
+fragment	C4H8O4	120.0422587
+fragment	C5H10O4	134.0579088
+fragment	C5H13O4N	151.0844579
+fragment	C6H11O4N	161.0688078
+fragment	C6H11O5N	177.0637225
+fragment	C6H13O5N	179.0793725
+fragment	C5H10O5	150.0528234
+fragment	C5H10O6	166.047738
+fragment	C5H12O2	104.0837296
+fragment	-(C5H12O2)-(H2O)	122.0942943
+fragment	C5H5N5	135.0544952
+fragment	C5H5ON5	151.0494098
+fragment	C5H6O2	98.03677943
+fragment	C5H7O2N5	169.0599745
+fragment	-(C5H7O3N)-(CO2)	173.0324223
+fragment	-(C5H7O3N)-(H2O)	147.0531578
+fragment	C5H8N3	110.0718223
+fragment	C5H8O3	116.0473441
+fragment	C5H8O5N5P	249.026305
+fragment	C5H9O3	117.0551691
+fragment	C5H9O6P	196.0136746
+fragment	C5H9O7P	212.0085893
+fragment	C6H10O3	130.0629942
+fragment	-(C6H10O3)-(H2O)	148.0735589
+fragment	C6H11O4N3PS	252.0207885
+fragment	C6H11O4NPS	224.0146405
+fragment	C6H12O5	164.0684735
+fragment	C6H14O6	182.0790382
+fragment	C6H14O7	198.0739528
+fragment	C6H16O7	200.0896029
+fragment	C6H16O8	216.0845175
+fragment	C6H8N3	122.0718223
+fragment	C6H8NS	126.0377453
+fragment	C7H5ON5	175.0494098
+fragment	C7H6ON6	190.0603088
+fragment	C7H7O2N5	193.0599745
+fragment	C7H11O6N	205.0586371
+fragment	C8H14O7	222.0739528
+fragment	C8H5O3N5	219.039239
+fragment	C8H7O4N5	237.0498037
+fragment	C9H10O4N2	210.0640568
+fragment	C9H11O3N3	209.0800412
+fragment	C9H11O4N3	225.0749558
+fragment	C9H12O5N2	228.0746215
+fragment	C9H12O6N3P	289.0463717
+fragment	C9H13O4N3	227.0906059
+fragment	C9H14O7N3P	307.0569364
+fragment	C9H16O8	252.0845175
+fragment	CH2N2	42.02179806
+fragment	-(CH2O)-(H2O)	48.02112937
+fragment	CH5NO	47.03711378
+fragment	-(H3PO4)-(CHNO)	140.9827089
+fragment	-(H3PO4)-(H2O)	115.9874599
+fragment	-(H3PO4)-(NH3)	115.0034443
+fragment	HPO3	79.96633052
diff -r bcf48aff1077 -r 573520b2e3b0 ACF/data/default_list_GC.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ACF/data/default_list_GC.csv	Tue Dec 17 10:47:31 2019 +0000
@@ -0,0 +1,111 @@
+isotope;13C db ;0.501677419
+isotope;13C;1.003354838
+isotope;15N;0.997034893
+isotope;18O;2.00424638
+isotope;34S;1.9957959
+isotope;41K;1.99811908
+isotope;37Cl;1.99704991
+isotope;13C2;2.006709676
+isotope;13C3;3.010064513
+isotope;13C+37Cl;3.000404748
+isotope;13C+18O;3.007601218
+isotope;13C+34S;2.999150738
+isotope;44Ca;3.99289082
+pertes;.H;1.007276432
+pertes;.CH3;15.0229265
+pertes;.CH2CH3;29.03857656
+pertes;.OCH3;31.01784112
+pertes;.CH2CH2CH3;43.05422662
+pertes;.OCH2CH3;45.03349118
+pertes;.CH2CH2CH2CH3;57.06987669
+pertes;H2;2.015650064
+pertes;H2O;18.01056468
+pertes;CO;27.99491462
+pertes;C2H4;28.03130013
+pertes;CH3OH;32.02621475
+pertes;CO2;43.98982924
+pertes;CH3CO2H;60.02112937
+pertes;HOSi(CH3)3;90.05009147
+fragments;.H;1.007276432
+fragments;.CH3;15.0229265
+fragments;.NH2;16.01817546
+fragments;.OH;17.00219105
+fragments;.NH3;17.0260005
+fragments;.F;18.99785462
+fragments;.CN;26.0025254
+fragments;.C2H3;27.0229265
+fragments;.C2H5;29.03857656
+fragments;CHO;29.00273965
+fragments;.CH3NH;30.03382553
+fragments;CH2NH2;30.03437413
+fragments;.CH3O;31.01784112
+fragments;.CH2OH;31.01784112
+fragments;.SH;32.97934743
+fragments;CH2F;33.01405328
+fragments;(H2O+CH3);48.02112937
+fragments;.Cl;34.96830408
+fragments;.CH2CN;40.01817546
+fragments;.C3H5;41.03857656
+fragments;.C3H7;43.05422662
+fragments;.CH3CO;43.01784112
+fragments;C2H5NH;44.05002419
+fragments;C2H5CO;57.03403978
+fragments;.COOH;44.99710567
+fragments;.NO2;45.99235464
+fragments;.CH2SH;46.9949975
+fragments;.CH2Cl;48.98395414
+fragments;.CHF2;51.00408287
+fragments;.CH2CH2CN;54.03382553
+fragments;.C4H7;55.05422662
+fragments;.C3H3O;55.01784112
+fragments;C4H9;57.07042529
+fragments;.C3H3O;55.01784112
+fragments;.C4H9;57.06987669
+fragments;.C3H5O;57.03349118
+fragments;.C3H8N;58.06512566
+fragments;.C3H7O;59.04914124
+fragments;.COOCH3;59.01275574
+fragments;.CH2COOH;59.01275574
+fragments;.C2H5S;61.01064756
+fragments;.C5H5;65.03857656
+fragments;.CF3;68.99466106
+fragments;.C4H7O;71.04914124
+fragments;.C6H5;77.03857656
+fragments;.Br;78.9177885
+fragments;.C6H7;79.05422662
+fragments;.C6H9;81.06987669
+fragments;.C5H5O;81.03349118
+fragments;.C7H7;91.05422662
+fragments;.C7H5O;105.0334912
+fragments;.C8H9;105.0698767
+fragments;.I;126.9039244
+fragments;H2;2.015650064
+fragments;NH3;17.0265491
+fragments;H2O;18.01056468
+fragments;HF;20.00622825
+fragments;HCN;27.01089903
+fragments;CO;27.99491462
+fragments;C2H4;28.03130013
+fragments;CH2O;30.01056468
+fragments;CH5N;31.04219916
+fragments;CH4O;32.02621475
+fragments;H2S;33.98772106
+fragments;HCl;35.97667771
+fragments;C3H6;42.04695019
+fragments;C2H2O;42.01056468
+fragments;CO2;43.98982924
+fragments;C2H7N;45.05784922
+fragments;C2H6O;46.04186481
+fragments;CH4S;48.00337113
+fragments;C4H6;54.04695019
+fragments;C4H8;56.06260026
+fragments;C3H4O;56.02621475
+fragments;C3H6O;58.04186481
+fragments;C3H9N;59.07349929
+fragments;C3H8O;60.05751488
+fragments;C2H4O2;60.02112937
+fragments;C2H6S;62.01902119
+fragments;C3H6O2;74.03677943
+fragments;C6H4;76.03130013
+fragments;C6H6;78.04695019
+fragments;HBr;79.92616213
diff -r bcf48aff1077 -r 573520b2e3b0 ACF/data/default_list_LC.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ACF/data/default_list_LC.csv	Tue Dec 17 10:47:31 2019 +0000
@@ -0,0 +1,225 @@
+adduit	-2H+Na+K	59.9378259
+adduit	H	1.007825032
+adduit	-H+K	37.95588165
+adduit	-H+Na	21.98194425
+adduit	-3H+3Na	65.94583274
+adduit	-4H+4K	151.8235266
+adduit	-4H+4Na	87.92777699
+adduit	-3H+3K	113.8676449
+adduit	-2H+2K	75.9117633
+adduit	-2H+2Na	43.9638885
+adduit	2H 	2.015650064
+adduit	Cl 	34.96885268
+adduit	-2H+Ca 	37.94694092
+isotope	13C db 	0.501677419
+isotope	13C	1.003354838
+isotope	15N	0.997034893
+isotope	18O	2.00424638
+isotope	34S	1.9957959
+isotope	41K	1.99811908
+isotope	37Cl	1.99704991
+isotope	13C2	2.006709676
+isotope	13C3	3.010064513
+isotope	13C+37Cl	3.000404748
+isotope	13C+18O	3.007601218
+isotope	13C+34S	2.999150738
+isotope	44Ca	3.99289082
+adduit	CH3OH	32.02621475
+adduit	CH3CN	41.0265491
+adduit	H2O	18.01056468
+adduit	2(H2O	36.02112937
+adduit	NaCl 	57.95862196
+adduit	HCOOH	46.0054793
+adduit	+(HCOOH)+(HCOOK)	129.9668403
+adduit	+(HCOOH)+(HCOONa)	113.9929029
+adduit	+(HCOOH)+2(HCOONa)	181.9803264
+adduit	HCOOK	83.96136095
+adduit	+(HCOOK)+(HCOONa)	151.9487845
+adduit	HCOONa	67.98742355
+adduit	2(HCOOH)	92.01095861
+adduit	+2(HCOOH)+(HCOOK)	175.9723196
+adduit	+2(HCOOH)+(HCOONa)	159.9983822
+adduit	2(HCOOK)	167.9227219
+adduit	2(HCOONa)	135.9748471
+fragment	C11H18O9	294.0950822
+fragment	C12H16O12	352.064176
+fragment	C12H20O9	308.1107322
+fragment	C2H2O	42.01056468
+fragment	C2H3.	27.0229265
+fragment	C2H3N	41.0265491
+fragment	C2H3NO3	89.01129296
+fragment	C2H3O.	43.01784112
+fragment	C2H4	28.03130013
+fragment	C2H4N.	42.03382553
+fragment	C2H4O	44.02621475
+fragment	C2H5.	29.03857656
+fragment	C2H5N	43.04219916
+fragment	C2H5NO2	75.0320284
+fragment	C2H5O.	45.03349118
+fragment	C2H5O6P	155.9823745
+fragment	C2H6	30.04695019
+fragment	C2H7N	45.05784922
+fragment	C2HNO2	71.00072827
+fragment	C3H4O3	88.01604399
+fragment	C3H5.	41.03857656
+fragment	C3H5NO2	87.0320284
+fragment	-(C3H5O2NS)-(NH3)	136.0306485
+fragment	C3H5O2NS	119.0040994
+fragment	C3H6	42.04695019
+fragment	C3H6O3	90.03169405
+fragment	C3H7.	43.05422662
+fragment	C3H7O2N	89.04767846
+fragment	C3H7O2NS	121.0197495
+fragment	C3H7O6P	169.9980246
+fragment	C4H6	54.04695019
+fragment	C4H6O2	86.03677943
+fragment	C4H6O4	118.0266087
+fragment	C4H7.	55.05422662
+fragment	C4H8O3	104.0473441
+fragment	C4H9	57.07042529
+fragment	C5H7O3N	129.0425931
+fragment	C5H8O3NS	162.0224891
+fragment	C5H8O4	132.0422587
+fragment	C6H10O4	146.0579088
+fragment	-(C6H10O5)-(H2O)	180.0633881
+fragment	C6H10O5	162.0528234
+fragment	C6H10O7	194.0426527
+fragment	C6H8O6	176.032088
+fragment	CH2O	30.01056468
+fragment	-(CH2S)-(HCOOH)	91.99320037
+fragment	-(CH2S)-(NH3)	63.01427016
+fragment	CH2S	45.98772106
+fragment	CH3.	15.0229265
+fragment	CH3COO.	59.01275574
+fragment	CH3COOH	60.02112937
+fragment	CH3N	29.0265491
+fragment	CH3O.	31.01784112
+fragment	CH3OH	32.02621475
+fragment	CH4	16.03130013
+fragment	CH4N.	30.03382553
+fragment	-(CH4S)-(HCOOH)	94.00885043
+fragment	-(CH4S)-(NH3)	65.02992022
+fragment	CH4S	48.00337113
+fragment	CH5N	31.04219916
+fragment	Cl.	34.96830408
+fragment	CO	27.99491462
+fragment	-(CO2)-(CO)	71.98474386
+fragment	CO2	43.98982924
+fragment	-(H2)-(NH3)	19.04219916
+fragment	H2	2.015650064
+fragment	-(H2O)-(CO2)	62.00039392
+fragment	-(H2O)-(HCOOH)	64.01604399
+fragment	-(H2O)-(NH3)	35.03711378
+fragment	H2O	18.01056468
+fragment	-(H2O)-2(CO2)	105.9902232
+fragment	-(H2S)-(H2O)	51.99828575
+fragment	H2S	33.98772106
+fragment	H2SO4	97.96737954
+fragment	H3PO4	97.97689521
+fragment	HCl	35.97667771
+fragment	HCN	27.01089903
+fragment	-(HCOOH)-(HCN)	73.01637834
+fragment	HCOOH	46.0054793
+fragment	HS.	32.97934743
+fragment	-(NC3H9)-(CH3COOH)	119.0946287
+fragment	-(NC3H9)-(H2O)	77.08406397
+fragment	-(NC3H9)-(HCOOH)	105.0789786
+fragment	NC3H9	59.07349929
+fragment	NaCl	57.95862196
+fragment	NH2CO.	44.01309008
+fragment	-(NH3)-(CO2)-(H2O)	79.02694302
+fragment	-(NH3)-(CO2)	61.01637834
+fragment	-(NH3)-(CONH)	60.03236275
+fragment	-(NH3)-(HCOOH)	63.0320284
+fragment	NH3	17.0265491
+fragment	NH3CO	45.02146372
+fragment	NHCO	43.00581365
+fragment	OH.	17.00219105
+fragment	PO3	78.95850549
+fragment	SO2	63.96190024
+fragment	SO3	79.95681486
+fragment	-2(H2O)-(CO2)	80.01095861
+fragment	-2(H2O)-(HCOOH)-(NH3)	99.05315777
+fragment	-2(H2O)-(HCOOH)	82.02660867
+fragment	2(H2O)	36.02112937
+fragment	2(HCOOH)	92.01095861
+fragment	-2(NH3)-(CO)-(CO2)	106.0378421
+fragment	-2(NH3)-(CO)	62.04801281
+fragment	2(NH3)	34.05309819
+fragment	3(H2O)	54.03169405
+fragment	3(NH3)	51.07964729
+fragment	4(H2O)	72.04225874
+fragment	C10H11O3N5	249.0861892
+fragment	C10H13O4N5	267.0967539
+fragment	C10H14O7N5P	347.0630844
+fragment	C10H15O5N5	285.1073186
+fragment	C2H3NO2	73.01637834
+fragment	C2H4O2	60.02112937
+fragment	C2H5NO3	91.02694302
+fragment	C2H6O2	62.03677943
+fragment	C2H6O3	78.03169405
+fragment	-(C2H6O3)-(H2O)	96.04225874
+fragment	C2H6O4	94.02660867
+fragment	C2H7NO2	77.04767846
+fragment	C3H10O5	126.0528234
+fragment	-(C3H6O3)-(CHNO)	133.0375077
+fragment	C3H6O4	106.0266087
+fragment	C3H8O3	92.04734412
+fragment	C3H8O4	108.0422587
+fragment	C4H10O5	138.0528234
+fragment	C4H5NO3	115.026943
+fragment	C4H8O4	120.0422587
+fragment	C5H10O4	134.0579088
+fragment	C5H13O4N	151.0844579
+fragment	C6H11O4N	161.0688078
+fragment	C6H11O5N	177.0637225
+fragment	C6H13O5N	179.0793725
+fragment	C5H10O5	150.0528234
+fragment	C5H10O6	166.047738
+fragment	C5H12O2	104.0837296
+fragment	-(C5H12O2)-(H2O)	122.0942943
+fragment	C5H5N5	135.0544952
+fragment	C5H5ON5	151.0494098
+fragment	C5H6O2	98.03677943
+fragment	C5H7O2N5	169.0599745
+fragment	-(C5H7O3N)-(CO2)	173.0324223
+fragment	-(C5H7O3N)-(H2O)	147.0531578
+fragment	C5H8N3	110.0718223
+fragment	C5H8O3	116.0473441
+fragment	C5H8O5N5P	249.026305
+fragment	C5H9O3	117.0551691
+fragment	C5H9O6P	196.0136746
+fragment	C5H9O7P	212.0085893
+fragment	C6H10O3	130.0629942
+fragment	-(C6H10O3)-(H2O)	148.0735589
+fragment	C6H11O4N3PS	252.0207885
+fragment	C6H11O4NPS	224.0146405
+fragment	C6H12O5	164.0684735
+fragment	C6H14O6	182.0790382
+fragment	C6H14O7	198.0739528
+fragment	C6H16O7	200.0896029
+fragment	C6H16O8	216.0845175
+fragment	C6H8N3	122.0718223
+fragment	C6H8NS	126.0377453
+fragment	C7H5ON5	175.0494098
+fragment	C7H6ON6	190.0603088
+fragment	C7H7O2N5	193.0599745
+fragment	C7H11O6N	205.0586371
+fragment	C8H14O7	222.0739528
+fragment	C8H5O3N5	219.039239
+fragment	C8H7O4N5	237.0498037
+fragment	C9H10O4N2	210.0640568
+fragment	C9H11O3N3	209.0800412
+fragment	C9H11O4N3	225.0749558
+fragment	C9H12O5N2	228.0746215
+fragment	C9H12O6N3P	289.0463717
+fragment	C9H13O4N3	227.0906059
+fragment	C9H14O7N3P	307.0569364
+fragment	C9H16O8	252.0845175
+fragment	CH2N2	42.02179806
+fragment	-(CH2O)-(H2O)	48.02112937
+fragment	CH5NO	47.03711378
+fragment	-(H3PO4)-(CHNO)	140.9827089
+fragment	-(H3PO4)-(H2O)	115.9874599
+fragment	-(H3PO4)-(NH3)	115.0034443
+fragment	HPO3	79.96633052
diff -r bcf48aff1077 -r 573520b2e3b0 ACF/lib/IonFiltration.pm
--- a/ACF/lib/IonFiltration.pm	Wed Oct 30 10:50:07 2019 -0400
+++ b/ACF/lib/IonFiltration.pm	Tue Dec 17 10:47:31 2019 +0000
@@ -77,9 +77,10 @@
 	my %hheader_line;
 	my %hrtmz;
 	
-	open (F5, $combined_DMVM);
+	open (F5, $combined_DMVM) or die "Impossible to open $file\n";
 	while(my $line = <F5>){
 		chomp $line;
+		
 		my @tline = split(/\t/, $line);
 		
 		if($linenb3 == 0){