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

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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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6 changes: 2 additions & 4 deletions tools/mfassignr/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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"
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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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8 changes: 5 additions & 3 deletions tools/mfassignr/mfassignr_snplot.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="mfassignr_snplot" name="MFAssignR SNplot" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<tool id="mfassignr_snplot" name="MFAssignR SNplot" version="@TOOL_VERSION@+galaxy1" profile="23.0">
<description>Noise level assessment using the SNplot function.</description>
<macros>
<import>macros.xml</import>
Expand All @@ -14,9 +14,11 @@
]]></command>
<configfiles>
<configfile name="run_script"><![CDATA[
cut = $sn_ratio * $kmdn

SNplot <- MFAssignR::SNplot(
df = read.delim("$input_file", sep="\t"),
cut = $cut,
cut = cut,
mass = $mass,
window.x = $window_x,
window.y = $window_y
Expand All @@ -34,7 +36,7 @@
<tests>
<test>
<param name="input_file" value="QC1_1_POS_500.tabular"/>
<param name="cut" value="3294705.63963789"/>
<param name="kmdn" value="549117.606606315"/>
<param name="mass" value="300"/>
<output name="SNplot" ftype="png" file="snplot/plot.png" />
</test>
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