From 2e23ebf0d77fd5fcd90508caed444a1b936a0335 Mon Sep 17 00:00:00 2001
From: KristinaGomoryova <gomoryova@sci.muni.cz>
Date: Wed, 16 Oct 2024 12:33:03 +0200
Subject: [PATCH] signal-to-noise separated into ratio and noise in IsoFiltR

---
 tools/mfassignr/macros.xml             | 3 +--
 tools/mfassignr/mfassignr_isofiltr.xml | 4 +++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tools/mfassignr/macros.xml b/tools/mfassignr/macros.xml
index 166a489f..5a307cc2 100644
--- a/tools/mfassignr/macros.xml
+++ b/tools/mfassignr/macros.xml
@@ -140,8 +140,7 @@
     <xml name="isofiltr_param">
         <param name="peaks" type="data" format="tabular" label="Input Peak Data"
         help="The input data frame containing abundance and peak mass."/>
-        <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio"
-        help="Sets the noise cut for the data; peaks below this value will not be evaluated."/>
+        <expand macro="noise_threshold_params" />
         <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio"
         help="Sets the maximum allowed ratio for matching 13C isotopes."/>
         <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio"
diff --git a/tools/mfassignr/mfassignr_isofiltr.xml b/tools/mfassignr/mfassignr_isofiltr.xml
index cf0423d2..b34709d2 100644
--- a/tools/mfassignr/mfassignr_isofiltr.xml
+++ b/tools/mfassignr/mfassignr_isofiltr.xml
@@ -21,9 +21,11 @@
     <configfiles>
         <configfile name="mfassignr_isofiltr"><![CDATA[
             peaks <- read.table("$peaks", header=TRUE, sep="\t")
+            SN = $sn_ratio * $kmdn
+
             result <- MFAssignR::IsoFiltR(
                 peaks = peaks,
-                SN = $SN,
+                SN = SN,
                 Carbrat = $Carbrat,
                 Sulfrat = $Sulfrat,
                 Sulferr = $Sulferr,