added parameters to MFAssignCHO

RECETOX · Oct 16, 2024 · f70d3f0 · f70d3f0
1 parent 9432288
commit f70d3f0
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diff --git a/tools/mfassignr/macros.xml b/tools/mfassignr/macros.xml
@@ -94,6 +94,42 @@
                help= "Lower limit of molecular mass to be assigned."/>
         <param name="highMW" type="float" label="Upper limit of molecular mass to be assigned" value="1000"
                help= "Upper limit of molecular mass to be assigned."/>
+        <param name="POEx" optional = "true" type="float" label="POEx" value="0"
+               help= "If set to 1 and ionMode is positive, positive mode odd electron ions can be assigned."/>              
+        <param name="NOEx" optional = "true" type="float" label="NOEx" value="0"
+               help= "If set to 1 and ionMode is negative, negative mode odd electron ions can be assigned."/> 
+        <param name="Ex" optional = "true" type="float" label="Ex" value="0" help= "Sets the amount of Chlorine 37 to be used in assignment."/>  
+        <param name="Mx" optional = "true" type="float" label="Mx" value="0" help= "Sets the amount of Sodium adduct to be used in assignment."/>       
+        <param name="NH4x" optional = "true" type="float" label="NH4x" value="0" help= "Sets the amount of Ammonium adduct to be used in assignment."/>     
+        <param name="Zx" optional = "true" type="float" label="Zx" value="0" help= "Sets the amount of charge to be used in assignment."/>    
+        <param name="Ox" optional = "true" type="float" label="Ox" value="0" help= "Sets the maximum number of oxygen looked for in the CHOFIT core, it limits the number of loops performed."/>  
+        <param name="O_Cmin" optional = "true" type="float" label="O_Cmin" value="0" help= "Sets the minimum allowed oxygen to carbon ratio."/> 
+        <param name="O_Cmax" optional = "true" type="float" label="O_Cmax" value="2.5" help= "Sets the upper limit for oxygen to carbon ratio."/> 
+        <param name="H_Cmin" optional = "true" type="float" label="H_Cmin" value="0.1" help= "Sets the lower limit for hydrogen to carbon ratio."/>     
+        <param name="H_Cmax" optional = "true" type="float" label="H_Cmax" value="3" help= "Sets the upper limit for hydrogen to carbon ratio for assigned formulas."/>          
+        <param name="DBEOmin" optional = "true" type="float" label="DBEOmin" value="-13" help= "Sets the lower limit for DBE minus oxygen QA parameter."/>
+        <param name="DBEOmax" optional = "true" type="float" label="DBEOmax" value="13" help= "Sets the upper limit for DBE minus oxygen QA parameter."/>    
+        <param name="Omin" optional = "true" type="float" label="Omin" value="0" help= "Sets the lower limit for oxygen number in assigned formula."/>    
+        <param name="max_def" optional = "true" type="float" label="max_def" value="0.9" help= "Sets the upper limit of mass defect for using floor() instead of round() for KMD."/>      
+        <param name="min_def" optional = "true" type="float" label="min_def" value="0.5" help= "Sets the lower limit of mass defect for using floor() instead of round() for KMD."/>  
+        <param name = "HetCut" optional = "true" type="select" display="radio" label="HetCut" help= "HetCut turns on or off the high heteroatom QA parameter.">
+              <option value="on">on</option>
+              <option value="off" selected="true">off</option> 
+        </param>  
+        <param name = "NMScut" optional = "true" type="select" display="radio" label="NMScut" help= "NMScut turns on or off the nominal mass series QA parameter.">
+              <option value="on" selected="true">on</option>
+              <option value="off">off</option> 
+        </param>  
+        <param name="DeNovo" optional = "true" type="float" label="DeNovo" value="1000" help= "Sets the de novo cut point for the data."/>  
+        <param name="nLoop" optional = "true" type="float" label="nLoop" value="5" help= "Sets the number of times the KMD and z* series assignment loops."/>  
+        <param name="Ambig" optional = "true" type="select" display="radio" label="Ambig" help= "Turns on or off increased ambiguity for assignment.">
+              <option value="on">on</option>
+              <option value="off" selected="true">off</option> 
+        </param> 
+        <param name = "MSMS" optional = "true" type="select" display="radio" label="MSMS" help= "Turns on or off CH2 KMD prescreening before initial assignment.">
+              <option value="on" >on</option>
+              <option value="off" selected="true">off</option> 
+        </param>
     </xml>
 
     <xml name="findrecalseries_param">

diff --git a/tools/mfassignr/mfassignr_mfassignCHO.xml b/tools/mfassignr/mfassignr_mfassignCHO.xml
@@ -32,7 +32,29 @@
             lowMW = $lowMW,
             highMW = $highMW,
             ppm_err = $ppm_err,
-            SN = SN
+            SN = SN,
+            POEx = $POEx, 
+            NOEx = $NOEx,
+            Ex = $Ex,
+            Mx = $Mx,
+            NH4x = $NH4x,
+            Zx = $Zx,
+            Ox = $Ox,
+            O_Cmin = $O_Cmin,
+            O_Cmax = $O_Cmax,
+            H_Cmin = $H_Cmin,
+            H_Cmax = $H_Cmax,
+            DBEOmin = $DBEOmin,
+            DBEOmax = $DBEOmax,
+            Omin = $Omin,
+            max_def = $max_def,
+            min_def = $min_def,
+            HetCut = $HetCut,
+            NMScut = $NMScut,
+            DeNovo = $DeNovo,
+            nLoop = $nLoop,
+            Ambig = $Ambig,
+            MSMS = $MSMS
         )
 
         write.table(MF_CHO_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t")