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signal-to-noise separated into ratio and noise in IsoFiltR #594

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merged 4 commits into from
Oct 21, 2024
Merged

signal-to-noise separated into ratio and noise in IsoFiltR #594

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2e23ebf
signal-to-noise separated into ratio and noise in IsoFiltR
KristinaGomoryova Oct 16, 2024
2778854
tool version updated
KristinaGomoryova Oct 17, 2024
cc5048d
cut parameter is splitted into sn_ratio and kmdn similarly as in othe…
KristinaGomoryova Oct 21, 2024
c55a1af
kmdn value in test updated
KristinaGomoryova Oct 21, 2024
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3 changes: 1 addition & 2 deletions tools/mfassignr/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
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6 changes: 4 additions & 2 deletions tools/mfassignr/mfassignr_isofiltr.xml
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Original file line number Diff line number Diff line change
@@ -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>
Expand All @@ -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,
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