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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 16:03:37 +0000
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51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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1 <tool id="xcms_plot_eic" name="xcms plot eic" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>Plot the extracted ion chromatogram (EIC) from mzML file</description>
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3 <macros>
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4 <import>macros_xcms_plot.xml</import>
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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5 </macros>
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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6 <expand macro="bio.tools"/>
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7 <expand macro="creator"/>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 Rscript -e 'source("${plot_eic}")'
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13 ]]></command>
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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14 <configfiles>
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15 <configfile name="plot_eic">
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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16 library(xcms)
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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17 library(MsExperiment)
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18 library(Spectra)
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19 mse = readMsExperiment(file.path('${input}'))
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20 offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
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21 chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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22 png(filename = '${output_filename}')
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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23 plot(chr)
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24 dev.off()
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25 </configfile>
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26 </configfiles>
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27 <inputs>
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28 <expand macro="base_params"/>
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29 <param type="integer" value="1" name="mslevel" min="1" label="MS Level" help="MS level for the EIC"/>
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30 </inputs>
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31 <outputs>
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32 <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier" />
51015f22fcb7 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" value="xcms_plot_eic_testdata.mzML"/>
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37 <param name="mz_value" value="153.06614"/>
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38 <param name="tolerance_ppm" value="10"/>
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39 <param name="mslevel" value="1"/>
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40 <output name="output_filename" file="eic_plot.png" compare="sim_size"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 This tool plots the extracted ion chromatogram (EIC) from an mzML file, using a provided m/z value.
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45 It uses a default tolerance of 10 ppm and operates at mslevel 1 by default.
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46 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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47 ]]></help>
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48 <expand macro="citations"/>
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49 </tool>