changeset 23:2a4a811c663d draft

planemo upload commit bf9996f1e380af6f783cc862f3e1d69f8c7b86e5
author lecorguille
date Mon, 14 Nov 2016 16:38:59 -0500
parents 65e3e1a39e16
children 10176a940ec6
files README.rst abims_CAMERA_annotateDiffreport.xml lib.r test-data/CASMI_extended_NEG_rules.csv test-data/CASMI_extended_POS_rules.csv
diffstat 5 files changed, 13 insertions(+), 485 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Fri Jul 22 11:25:17 2016 -0400
+++ b/README.rst	Mon Nov 14 16:38:59 2016 -0500
@@ -2,10 +2,6 @@
 Changelog/News
 --------------
 
-**Version 2.1.6 - 06/07/2016**
-
-- IMPROVEMENT: add the possibility to use defined ruleset
-
 **Version 2.1.5 - 21/04/2016**
 
 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
--- a/abims_CAMERA_annotateDiffreport.xml	Fri Jul 22 11:25:17 2016 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Mon Nov 14 16:38:59 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.6">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
@@ -33,11 +33,7 @@
             calcCiS $quick_block.calcCiS
             calcIso $quick_block.calcIso
             calcCaS $quick_block.calcCaS
-            #if $quick_block.rules_block.rules_select == "FALSE"
-                multiplier $quick_block.rules_block.multiplier
-            #else
-                rules $quick_block.rules_block.rules
-            #end if
+            multiplier $quick_block.multiplier
         #end if
 
         #if $options.option == "show":
@@ -98,24 +94,14 @@
                 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/>
                 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
                 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/>
-                <conditional name="rules_block">
-                    <param name="rules_select" type="select" label="Use a personal ruleset file">  
-                        <option value="TRUE">TRUE</option>
-                        <option value="FALSE" selected="true">FALSE</option>
-                    </param>
-                    <when value="FALSE">
-                        <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> 
-                    </when>
-                    <when value="TRUE">
-                        <param name="rules" type="data" format="csv" label="findAdducts: User defined ruleset" help="[rules]" />
-                    </when>
-                </conditional>
+                <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" />
             </when>	
-            <when value="TRUE">
+                <when value="TRUE">
                 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
             </when>	
         </conditional>
-
+                           
+    
         <!-- Annotatediffreport specific parameters -->
         <conditional name="options">
             <param name="option" type="select" label="Number of condition">
@@ -410,10 +396,6 @@
 Changelog/News
 --------------
 
-**Version 2.1.6 - 06/07/2016**
-
-- IMPROVEMENT: add the possibility to use defined ruleset
-
 **Version 2.1.5 - 21/04/2016**
 
 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
--- a/lib.r	Fri Jul 22 11:25:17 2016 -0400
+++ b/lib.r	Mon Nov 14 16:38:59 2016 -0500
@@ -25,42 +25,15 @@
   listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
   listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
   listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
-  
-  # common parameters
-  listArguments4annotate = list(object=xset,
-    nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],
-    maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],
-    ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],
-    polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
- 
-  # quick == FALSE
-  if(listArguments[["quick"]]==FALSE) {
-    listArguments4annotate = append(listArguments4annotate,
-        list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],
-        calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))
-    # no ruleset
-    if (!is.null(listArguments[["multiplier"]])) {
-        listArguments4annotate = append(listArguments4annotate,
-            list(multiplier=listArguments[["multiplier"]]))
-    }
-    # ruleset
-    else {
-        rulset=read.table(listArguments[["rules"]], h=T, sep=";")
-        if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t")
-        if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep=",")
-        if (ncol(rulset) < 4) {
-            error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
-            print(error_message)
-            stop(error_message)
-        }	
 
-        listArguments4annotate = append(listArguments4annotate,
-            list(rules=rulset))
-    }
+  #graphMethod parameter bugs where this parameter is not defined in quick=true
+  if(listArguments[["quick"]]==TRUE) {
+    xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
   }
-  
-  # launch annotate
-  xa = do.call("annotate", listArguments4annotate)
+  else {
+    xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]],multiplier=listArguments[["multiplier"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
+
+  }  
   peakList=getPeaklist(xa,intval=listArguments[["intval"]])
   peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
 
--- a/test-data/CASMI_extended_NEG_rules.csv	Fri Jul 22 11:25:17 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +0,0 @@
-"name","nmol","charge","massdiff","oidscore","quasi","ips"
-"[M-H]-",1,-1,-1.007276,1,1,1
-"[M-2H]2-",1,-2,-2.014552,2,0,1
-"[M-3H]3-",1,-3,-3.021828,3,0,1
-"[M-2H+Na]-",1,-1,20.974666,4,0,0.25
-"[M-H+Cl]2-",1,-2,33.962126,5,0,1
-"[M-2H+K]-",1,-1,36.948606,6,0,0.25
-"[M+Cl]-",1,-1,34.969402,7,1,1
-"[M+2Cl]2-",1,-2,69.938804,8,0,1
-"[2M-H]-",2,-1,-1.007276,1,0,0.5
-"[2M-2H]2-",2,-2,-2.014552,2,0,0.5
-"[2M-3H]3-",2,-3,-3.021828,3,0,0.5
-"[2M-2H+Na]-",2,-1,20.974666,4,0,0.25
-"[2M-H+Cl]2-",2,-2,33.962126,5,0,0.5
-"[2M-2H+K]-",2,-1,36.948606,6,0,0.25
-"[2M+Cl]-",2,-1,34.969402,7,0,0.5
-"[2M+2Cl]2-",2,-2,69.938804,8,0,0.5
-"[3M-H]-",3,-1,-1.007276,1,0,0.5
-"[3M-2H]2-",3,-2,-2.014552,2,0,0.5
-"[3M-3H]3-",3,-3,-3.021828,3,0,0.5
-"[3M-2H+Na]-",3,-1,20.974666,4,0,0.25
-"[3M-H+Cl]2-",3,-2,33.962126,5,0,0.5
-"[3M-2H+K]-",3,-1,36.948606,6,0,0.25
-"[3M+Cl]-",3,-1,34.969402,7,0,0.5
-"[3M+2Cl]2-",3,-2,69.938804,8,0,0.5
-"[M+Cl+NaCOOH]-",1,-1,102.956842,9,0,0.5
-"[M-H+NaCOOH]-",1,-1,66.980164,10,0,0.5
-"[M+Cl+HCOOH]-",1,-1,80.974872,11,0,0.5
-"[M+HCOO]-",1,-1,44.99765,12,0,1
-"[M+Cl+CF3COOH]-",1,-1,148.962402,13,0,0.5
-"[M-H+CF3COOH]-",1,-1,112.985724,14,0,0.5
-"[M+Cl+NH3]-",1,-1,51.995952,15,0,0.5
-"[M-H+NH3]-",1,-1,16.019274,16,0,0.5
-"[M-H-CH4]-",1,-1,-17.038576,17,0,0.25
-"[M-H-CO]-",1,-1,-29.002176,18,0,0.25
-"[M-H-C2H2O2]-",1,-1,-47.012746,19,0,0.25
-"[M-H-C3H2O3]-",1,-1,-87.007666,20,0,0.25
-"[M-H-C5H8O4]-",1,-1,-133.049536,21,0,0.25
-"[M-H-C6H10O4]-",1,-1,-147.065186,22,0,0.25
-"[M-H-C6H10O5]-",1,-1,-163.060096,23,0,0.25
-"[M-H-C6H8O6]-",1,-1,-177.039366,24,0,0.25
-"[M-H-H2]-",1,-1,-3.02292607,25,0,0.25
-"[M-H-CH2]-",1,-1,-15.02292607,26,0,0.25
-"[M-H-CH3]-",1,-1,-16.030751105,27,0,0.25
-"[M-H-NH3]-",1,-1,-18.033826,28,0,0.25
-"[M-H-H2O]-",1,-1,-19.0178407,29,0,0.25
-"[M-H-H4O2]-",1,-1,-37.0284054,30,0,0.25
-"[M-H-HF]-",1,-1,-21.013504255,31,0,0.25
-"[M-H-C2H2]-",1,-1,-27.02292607,32,0,0.25
-"[M-H-C2H3]-",1,-1,-28.030751105,33,0,0.25
-"[M-H-HCN]-",1,-1,-28.018175037,34,0,0.25
-"[M-H-C2H4]-",1,-1,-29.03857614,35,0,0.25
-"[M-H-C2H6]-",1,-1,-31.05422621,36,0,0.25
-"[M-H-CH2O]-",1,-1,-31.0178407,37,0,0.25
-"[M-H-CH5N]-",1,-1,-32.049475177,38,0,0.25
-"[M-H-CH4O]-",1,-1,-33.03349077,39,0,0.25
-"[M-H-H2S]-",1,-1,-34.99499677,40,0,0.25
-"[M-H-HCl]-",1,-1,-36.983953755,41,0,0.25
-"[M-H-C3H2]-",1,-1,-39.02292607,42,0,0.25
-"[M-H-C2N]-",1,-1,-39.010350002,43,0,0.25
-"[M-H-F2]-",1,-1,-39.00408244,44,0,0.25
-"[M-H-C3H3]-",1,-1,-40.030751105,45,0,0.25
-"[M-H-HC2N]-",1,-1,-40.018175037,46,0,0.25
-"[M-H-C3H4]-",1,-1,-41.03857614,47,0,0.25
-"[M-H-C3H6]-",1,-1,-43.05422621,48,0,0.25
-"[M-H-C2H2O]-",1,-1,-43.0178407,49,0,0.25
-"[M-H-C3H6]-",1,-1,-43.05422621,50,0,0.25
-"[M-H-NCO]-",1,-1,-43.005264632,51,0,0.25
-"[M-H-CN2H2]-",1,-1,-43.029074074,52,0,0.25
-"[M-H-HCNO]-",1,-1,-44.013089667,53,0,0.25
-"[M-H-C2H4O]-",1,-1,-45.03349077,54,0,0.25
-"[M-H-CO2]-",1,-1,-44.99710526,55,0,0.25
-"[M-H-N2O]-",1,-1,-45.008338634,56,0,0.25
-"[M-H-CONH2]-",1,-1,-45.020914702,57,0,0.25
-"[M-H-NC2H7]-",1,-1,-46.065125247,58,0,0.25
-"[M-H-C2H6O]-",1,-1,-47.04914084,59,0,0.25
-"[M-H-NO2]-",1,-1,-47.000179262,60,0,0.25
-"[M-H-CH4S]-",1,-1,-49.01064684,61,0,0.25
-"[M-H-C4H4]-",1,-1,-53.03857614,62,0,0.25
-"[M-H-C2N2]-",1,-1,-53.013424004,63,0,0.25
-"[M-H-C4H6]-",1,-1,-55.05422621,64,0,0.25
-"[M-H-C4H8]-",1,-1,-57.06987628,65,0,0.25
-"[M-H-C3H6O]-",1,-1,-59.04914084,66,0,0.25
-"[M-H-C4H10]-",1,-1,-59.08552635,67,0,0.25
-"[M-H-C2H5NO]-",1,-1,-60.044389807,68,0,0.25
-"[M-H-C3H8O]-",1,-1,-61.06479091,69,0,0.25
-"[M-H-C2H4O2]-",1,-1,-61.0284054,70,0,0.25
-"[M-H-C2H5Cl]-",1,-1,-65.015253895,71,0,0.25
-"[M-H-C5H4]-",1,-1,-65.03857614,72,0,0.25
-"[M-H-SO2]-",1,-1,-64.96917596,73,0,0.25
-"[M-H-C5H8]-",1,-1,-69.06987628,74,0,0.25
-"[M-H-C5H12]-",1,-1,-73.10117642,75,0,0.25
-"[M-H-C3H6O2]-",1,-1,-75.04405547,76,0,0.25
-"[M-H-C4H10O]-",1,-1,-75.08044098,77,0,0.25
-"[M-H-C6H6]-",1,-1,-79.05422621,78,0,0.25
-"[M-H-CS2]-",1,-1,-76.9514174,79,0,0.25
-"[M-H-C5H5N]-",1,-1,-80.049475177,80,0,0.25
-"[M-H-HBr]-",1,-1,-80.933437135,81,0,0.25
-"[M-H-C2F4]-",1,-1,-101.00088888,82,0,0.25
-"[M-H-C2F6]-",1,-1,-138.99769532,83,0,0.25
-"[M-H-C7H6O2]-",1,-1,-123.04405547,84,0,0.25
-"[M-H-HI]-",1,-1,-128.919574035,85,0,0.25
-"[M-H-H6O3]-",1,-1,-55.0389701,87,0,0.25
-"[M-H-H8O4]-",1,-1,-73.0495348,88,0,0.25
-"[M-H-H10O5]-",1,-1,-91.0600995,89,0,0.25
-"[M-H-H12O6]-",1,-1,-109.0706642,90,0,0.25
-"[M-H-H14O7]-",1,-1,-127.0812289,91,0,0.25
-"[M-H-CH6O3]-",1,-1,-67.0389701,93,0,0.25
-"[M-H-CH4O2]-",1,-1,-49.0284054,94,0,0.25
-"[M-H-NaOH]-",1,-1,-40.999783365,95,0,0.25
-"[M-H-KOH]-",1,-1,-56.973723065,96,0,0.25
--- a/test-data/CASMI_extended_POS_rules.csv	Fri Jul 22 11:25:17 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,312 +0,0 @@
-"name","nmol","charge","massdiff","oidscore","quasi","ips"
-"[M+H]+",1,1,1.007276,1,1,1
-"[M+2H]2+",1,2,2.014552,2,0,1
-"[M+3H]3+",1,3,3.021828,3,0,1
-"[M+H+Na]2+",1,2,23.996494,4,0,0.5
-"[M+H+K]2+",1,2,39.970434,6,0,0.5
-"[M+Na]+",1,1,22.989218,7,1,1
-"[M+2Na]2+",1,2,45.978436,8,0,0.75
-"[M+K]+",1,1,38.963158,9,1,1
-"[M+Na+K]2+",1,2,61.952376,10,0,0.75
-"[M+2Na+K]3+",1,3,84.941594,11,0,0.75
-"[M+2K]2+",1,2,77.926316,12,0,0.75
-"[M+Na+2K]3+",1,3,100.915534,13,0,0.75
-"[M+2Na-H]+",1,1,44.97116,15,0,0.25
-"[M+3Na-H]2+",1,2,67.960378,16,0,0.25
-"[M+Na+K-H]+",1,1,60.9451,17,0,0.25
-"[M+2Na+K-H]2+",1,2,83.934318,18,0,0.25
-"[M+3Na+K-H]3+",1,3,106.923536,19,0,0.25
-"[M+Na+2K-H]2+",1,2,99.908258,20,0,0.25
-"[M+2Na+2K-H]3+",1,3,122.897476,21,0,0.25
-"[M+2K-H]+",1,1,76.91904,23,0,0.25
-"[M+3K-H]2+",1,2,115.882198,24,0,0.25
-"[M+Na+3K-H]3+",1,3,138.871416,25,0,0.25
-"[2M+H]+",2,1,1.007276,1,0,0.5
-"[2M+2H]2+",2,2,2.014552,2,0,0.5
-"[2M+3H]3+",2,3,3.021828,3,0,0.5
-"[2M+H+Na]2+",2,2,23.996494,4,0,0.5
-"[2M+H+K]2+",2,2,39.970434,6,0,0.5
-"[2M+Na]+",2,1,22.989218,7,0,0.5
-"[2M+2Na]2+",2,2,45.978436,8,0,0.5
-"[2M+K]+",2,1,38.963158,9,0,0.5
-"[2M+Na+K]2+",2,2,61.952376,10,0,0.5
-"[2M+2Na+K]3+",2,3,84.941594,11,0,0.5
-"[2M+2K]2+",2,2,77.926316,12,0,0.5
-"[2M+Na+2K]3+",2,3,100.915534,13,0,0.5
-"[2M+2Na-H]+",2,1,44.97116,15,0,0.25
-"[2M+3Na-H]2+",2,2,67.960378,16,0,0.25
-"[2M+Na+K-H]+",2,1,60.9451,17,0,0.25
-"[2M+2Na+K-H]2+",2,2,83.934318,18,0,0.25
-"[2M+3Na+K-H]3+",2,3,106.923536,19,0,0.25
-"[2M+Na+2K-H]2+",2,2,99.908258,20,0,0.25
-"[2M+2Na+2K-H]3+",2,3,122.897476,21,0,0.25
-"[2M+2K-H]+",2,1,76.91904,23,0,0.25
-"[2M+3K-H]2+",2,2,115.882198,24,0,0.25
-"[2M+Na+3K-H]3+",2,3,138.871416,25,0,0.25
-"[3M+H]+",3,1,1.007276,1,0,0.5
-"[3M+2H]2+",3,2,2.014552,2,0,0.5
-"[3M+3H]3+",3,3,3.021828,3,0,0.5
-"[3M+H+Na]2+",3,2,23.996494,4,0,0.5
-"[3M+H+K]2+",3,2,39.970434,6,0,0.5
-"[3M+Na]+",3,1,22.989218,7,0,0.5
-"[3M+2Na]2+",3,2,45.978436,8,0,0.5
-"[3M+K]+",3,1,38.963158,9,0,0.5
-"[3M+Na+K]2+",3,2,61.952376,10,0,0.5
-"[3M+2Na+K]3+",3,3,84.941594,11,0,0.5
-"[3M+2K]2+",3,2,77.926316,12,0,0.5
-"[3M+Na+2K]3+",3,3,100.915534,13,0,0.5
-"[3M+2Na-H]+",3,1,44.97116,15,0,0.25
-"[3M+3Na-H]2+",3,2,67.960378,16,0,0.25
-"[3M+Na+K-H]+",3,1,60.9451,17,0,0.25
-"[3M+2Na+K-H]2+",3,2,83.934318,18,0,0.25
-"[3M+3Na+K-H]3+",3,3,106.923536,19,0,0.25
-"[3M+Na+2K-H]2+",3,2,99.908258,20,0,0.25
-"[3M+2Na+2K-H]3+",3,3,122.897476,21,0,0.25
-"[3M+2K-H]+",3,1,76.91904,23,0,0.25
-"[3M+3K-H]2+",3,2,115.882198,24,0,0.25
-"[3M+Na+3K-H]3+",3,3,138.871416,25,0,0.25
-"[M+Na+NaCOOH]+",1,1,90.976658,27,0,0.5
-"[M+K+NaCOOH]+",1,1,106.950598,28,0,0.5
-"[M+Na+HCOOH]+",1,1,68.994688,29,0,0.5
-"[M+K+HCOOH]+",1,1,84.968628,30,0,0.5
-"[M+H+HCOOH]+",1,1,47.012746,31,0,0.5
-"[M+Na+CF3COOH]+",1,1,136.982218,32,0,0.5
-"[M+K+CF3COOH]+",1,1,152.956158,33,0,0.5
-"[M+H+CF3COOH]+",1,1,115.000276,34,0,0.5
-"[M+Na+NH3]+",1,1,40.015768,35,0,0.5
-"[M+K+NH3]+",1,1,55.989708,36,0,0.5
-"[M+H+NH3]+",1,1,18.033826,37,0,0.5
-"[M+H-CH4]+",1,1,-15.024024,38,0,0.25
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-"[M+3H-CH4]3+",1,3,-13.009472,40,0,0.25
-"[M+H-CO]+",1,1,-26.987624,41,0,0.25
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-"[M+3H-CH3]3+",1,3,-12.001647105,70,0,0.25
-"[M+H-NH3]+",1,1,-16.019274,71,0,0.5
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-"[M+3H-C2H3]3+",1,3,-24.001647105,88,0,0.25
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-"[M+2H-HCN]2+",1,2,-24.996347037,90,0,0.25
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-"[M+3H-CH2O]3+",1,3,-26.9887367,100,0,0.25
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-"[M+3H-CH5N]3+",1,3,-28.020371177,103,0,0.25
-"[M+H-CH4O]+",1,1,-31.01893877,104,0,0.25
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-"[M+3H-CH4O]3+",1,3,-29.00438677,106,0,0.25
-"[M+H-H2S]+",1,1,-32.98044477,107,0,0.25
-"[M+2H-H2S]2+",1,2,-31.97316877,108,0,0.25
-"[M+3H-H2S]3+",1,3,-30.96589277,109,0,0.25
-"[M+H-HCl]+",1,1,-34.969401755,110,0,0.25
-"[M+2H-HCl]2+",1,2,-33.962125755,111,0,0.25
-"[M+3H-HCl]3+",1,3,-32.954849755,112,0,0.25
-"[M+H-C3H2]+",1,1,-37.00837407,113,0,0.25
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-"[M+3H-C2N]3+",1,3,-34.981246002,118,0,0.25
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-"[M+3H-C3H6]3+",1,3,-39.02512221,139,0,0.25
-"[M+H-NCO]+",1,1,-40.990712632,140,0,0.25
-"[M+2H-NCO]2+",1,2,-39.983436632,141,0,0.25
-"[M+3H-NCO]3+",1,3,-38.976160632,142,0,0.25
-"[M+H-CN2H2]+",1,1,-41.014522074,143,0,0.25
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-"[M+3H-CN2H2]3+",1,3,-38.999970074,145,0,0.25
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-"[M+H-C2H5NO]+",1,1,-58.029837807,191,0,0.25
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-"[M+H-C2H5Cl]+",1,1,-63.000701895,200,0,0.25
-"[M+2H-C2H5Cl]2+",1,2,-61.993425895,201,0,0.25
-"[M+3H-C2H5Cl]3+",1,3,-60.986149895,202,0,0.25
-"[M+H-C5H4]+",1,1,-63.02402414,203,0,0.25
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-"[M+H-NaOH]+",1,1,-38.985231365,272,0,0.25
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