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comparison xcms_plot_eic.xml @ 0:51015f22fcb7 draft

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