# HG changeset patch
# User recetox
# Date 1729501613 0
# Node ID f7a738bf392f85658345225f05905d752cddba5a
# Parent  ef0388b42f7a5019a58e7c351192b4711ae07868
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 4bd188e61f09431c0b7e73b35fb8ccf5ee7af6ac

diff -r ef0388b42f7a -r f7a738bf392f macros.xml
--- a/macros.xml	Mon Sep 16 09:06:41 2024 +0000
+++ b/macros.xml	Mon Oct 21 09:06:53 2024 +0000
@@ -68,8 +68,7 @@
     <xml name="snplot_param">
         <param name="input_file" type="data" format="tabular" label="Input data"
                help= "Input data frame, first column is mass, second column is intensity"/>
-        <param name="cut" type="float" label="cut" value="0"
-               help= "A numeric value of the intensity cut value being investigated"/>
+        <expand macro="noise_threshold_params" />
         <param name="mass" type="float" label="mass" value="300"
                help= "A numeric value setting a centerpoint to look at the mass spectrum"/>
         <param name="window_x" type="float" label="window.x" value="0.5"
@@ -140,8 +139,7 @@
     <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 -r ef0388b42f7a -r f7a738bf392f mfassignr_isofiltr.xml
--- a/mfassignr_isofiltr.xml	Mon Sep 16 09:06:41 2024 +0000
+++ b/mfassignr_isofiltr.xml	Mon Oct 21 09:06:53 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="mfassignr_isofiltr" name="MFAssignR IsoFiltR" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+<tool id="mfassignr_isofiltr" name="MFAssignR IsoFiltR" version="@TOOL_VERSION@+galaxy1" profile="23.0">
     <description>Separates likely isotopic masses from monoisotopic masses in a mass list</description>
     <macros>
         <import>macros.xml</import>
@@ -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,