Mercurial > repos > workflow4metabolomics > xcms_plot_eic

comparison xcms_plot_eic.xml @ 1:cbedca3ba6e1 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
author workflow4metabolomics
date Thu, 15 May 2025 17:02:59 +0000 (8 days ago)
parents 51015f22fcb7
children
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0:51015f22fcb7 1:cbedca3ba6e1
14 <configfiles> 14 <configfiles>
15 <configfile name="plot_eic"> 15 <configfile name="plot_eic">
16 library(xcms) 16 library(xcms)
17 library(MsExperiment) 17 library(MsExperiment)
18 library(Spectra) 18 library(Spectra)
19
20 sessionInfo()
21
19 mse = readMsExperiment(file.path('${input}')) 22 mse = readMsExperiment(file.path('${input}'))
20 offset = ${tolerance_ppm} * 1e-6 * ${mz_value} 23 offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
21 chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel}) 24 chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
22 png(filename = '${output_filename}') 25 png(filename = '${output_filename}')
23 plot(chr) 26 plot(chr)
24 dev.off() 27 dev.off()
25 </configfile> 28 </configfile>
26 </configfiles> 29 </configfiles>
27 <inputs> 30 <inputs>
28 <expand macro="base_params"/> 31 <expand macro="base_params"/>
29 <param type="integer" value="1" name="mslevel" min="1" label="MS Level" help="MS level for the EIC"/>
30 </inputs> 32 </inputs>
31 <outputs> 33 <outputs>
32 <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier" /> 34 <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier" />
33 </outputs> 35 </outputs>
34 <tests> 36 <tests>