From 712e0f00602de5ed873a98992701b60e2f4ad02a Mon Sep 17 00:00:00 2001 From: KristinaGomoryova Date: Fri, 18 Oct 2024 15:27:20 +0200 Subject: [PATCH] parameters for MFAssign/CHO restructured and updated --- tools/mfassignr/macros.xml | 63 ++++++++++++++++++++--- tools/mfassignr/mfassignr_mfassign.xml | 58 ++++++++++++++++++++- tools/mfassignr/mfassignr_mfassignCHO.xml | 4 +- 3 files changed, 115 insertions(+), 10 deletions(-) diff --git a/tools/mfassignr/macros.xml b/tools/mfassignr/macros.xml index 2d8aa58e..8221a53e 100644 --- a/tools/mfassignr/macros.xml +++ b/tools/mfassignr/macros.xml @@ -85,7 +85,7 @@ - + @@ -94,16 +94,21 @@ help= "Lower limit of molecular mass to be assigned."/> -
+ + + + + + + + + + - - - - - + @@ -131,6 +136,50 @@ + + + + +
+ + + +
+
+ + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
diff --git a/tools/mfassignr/mfassignr_mfassign.xml b/tools/mfassignr/mfassignr_mfassign.xml index c6732830..4d11765c 100644 --- a/tools/mfassignr/mfassignr_mfassign.xml +++ b/tools/mfassignr/mfassignr_mfassign.xml @@ -19,6 +19,19 @@ iso <- read.delim("$input_iso", sep="\t") #end if SN = $sn_ratio * $kmdn + POEx = 0 + NOEx = 0 + + #if "$assign_typeof_ions"=="yes" + #if $ionMode=="pos" + POEx = 1 + NOEx = 0 + #end if + #if $ionMode=="neg" + POEx = 0 + NOEx = 1 + #end if + #end if MF_assign <- MFAssignR::MFAssign( peaks = mono, @@ -29,7 +42,50 @@ lowMW = $lowMW, highMW = $highMW, ppm_err = $ppm_err, - SN = SN + SN = SN, + POEx = POEx, + NOEx = NOEx, + Nx = $Nx, + Sx = $Sx, + Px = $Px, + S34x = $S34x, + N15x = $N15x, + Dx = $Dx, + Clx = $Clx, + Fx = $Fx, + Cl37x = $Cl37x, + Br81x = $Br81x, + Ix = $Ix, + 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_bool", + MSMS = "$MSMS", + Sval = $Sval, + Nval = $Nval, + S34val = $S34val, + N15val = $N15val, + Pval = $Pval, + iso_err = $iso_err, + SulfCheck = "$SulfCheck", + S34_abund = $S34_abund, + C13_abund = $C13_abund, + N3corr = "$N3corr" ) write.table(MF_assign[['Unambig']], file = '$Unambig', row.names= FALSE, sep = "\t") diff --git a/tools/mfassignr/mfassignr_mfassignCHO.xml b/tools/mfassignr/mfassignr_mfassignCHO.xml index 27d4dd56..01e94ad3 100644 --- a/tools/mfassignr/mfassignr_mfassignCHO.xml +++ b/tools/mfassignr/mfassignr_mfassignCHO.xml @@ -24,7 +24,7 @@ SN = $sn_ratio * $kmdn POEx = 0 NOEx = 0 - + #if "$assign_typeof_ions"=="yes" #if $ionMode=="pos" POEx = 1 @@ -87,7 +87,7 @@ help= "Data frame containing monoisotopic masses, output from the IsoFiltR function"/> - +