+
−<tool id="xcms_plot_eic" name="xcms plot eic" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+
−    <description>Plot the extracted ion chromatogram (EIC) from mzML file</description>
+
−    <macros>
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−        <import>macros_xcms_plot.xml</import>
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−    </macros>
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−    <expand macro="bio.tools"/>
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−    <expand macro="creator"/>
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−    <requirements>
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−        <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
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−    </requirements>
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−    <command detect_errors="exit_code"><![CDATA[
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−        Rscript -e 'source("${plot_eic}")'
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−    ]]></command>
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−    <configfiles>
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−        <configfile name="plot_eic">
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−library(xcms)
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−library(MsExperiment)
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−library(Spectra)
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−mse = readMsExperiment(file.path('${input}'))
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−offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
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−chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
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−png(filename = '${output_filename}')
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−plot(chr)
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−dev.off()
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−        </configfile>
+
−    </configfiles>
+
−    <inputs>
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−        <expand macro="base_params"/>
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−        <param type="integer" value="1" name="mslevel" min="1" label="MS Level" help="MS level for the EIC"/>
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−    </inputs>
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−    <outputs>
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−        <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier"  />
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−    </outputs>
+
−    <tests>
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−        <test>
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−            <param name="input" value="xcms_plot_eic_testdata.mzML"/>
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−            <param name="mz_value" value="153.06614"/>
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−            <param name="tolerance_ppm" value="10"/>
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−            <param name="mslevel" value="1"/>
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−            <output name="output_filename" file="eic_plot.png" compare="sim_size"/>
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−        </test>
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−    </tests>
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−    <help><![CDATA[
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−        This tool plots the extracted ion chromatogram (EIC) from an mzML file, using a provided m/z value. 
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−        It uses a default tolerance of 10 ppm and operates at mslevel 1 by default.    
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−        More information and detailed instructions can be found in the tutorial at: https://jorainer.github.io/xcmsTutorials/articles/xcms-preprocessing.html#data-visualization
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−    ]]></help>
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−    <expand macro="citations"/>
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−</tool>