Mercurial > repos > workflow4metabolomics > xcms_plot_raw

comparison xcms_plot_raw.xml @ 1:8b8d360316c3 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 17:02:56 +0000
parents 520448a32548
children
comparison
equal deleted inserted replaced
0:520448a32548 1:8b8d360316c3
14 <configfiles> 14 <configfiles>
15 <configfile name="plot_raw"> 15 <configfile name="plot_raw">
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 mz_offset = ${tolerance_ppm} * 1e-6 * ${mz_value} 23 mz_offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
21 rt_offset = ${rt_range} / 2 24 rt_offset = ${rt_range}
25
22 raw = mse |> 26 raw = mse |>
27 filterMsLevel(msLevel = ${mslevel}L) |>
23 filterRt(rt = ${rt} + c(-rt_offset, rt_offset)) |> 28 filterRt(rt = ${rt} + c(-rt_offset, rt_offset)) |>
24 filterMzRange(mz = ${mz_value} + c(-mz_offset, mz_offset)) 29 filterMzRange(mz = ${mz_value} + c(-mz_offset, mz_offset))
25 png(filename = '${output_filename}') 30 png(filename = '${output_filename}')
26 par(oma = c(0.5, 2, 0.5, 1)) 31 par(oma = c(0.5, 2, 0.5, 1))
27 plot(raw) 32 plot(raw)
29 </configfile> 34 </configfile>
30 </configfiles> 35 </configfiles>
31 <inputs> 36 <inputs>
32 <expand macro="base_params"/> 37 <expand macro="base_params"/>
33 <param type="float" name="rt" label="Retention Time" min="0.0" value="0.0" help="Retention time for the plot"/> 38 <param type="float" name="rt" label="Retention Time" min="0.0" value="0.0" help="Retention time for the plot"/>
34 <param type="float" name="rt_range" value="5.0" min="0.0" label="Retention Time Range" help="Retention time range for the plot"/> 39 <param type="float" name="rt_range" value="5.0" min="0.0" label="Retention Time Range" help="Retention time range for the plot. Range is applied on both sides of the specified RT value (+-)."/>
35 </inputs> 40 </inputs>
36 <outputs> 41 <outputs>
37 <data name="output_filename" format="png" label="PLot at m/z=$mz_value and rt=$rt of $input.element_identifier"/> 42 <data name="output_filename" format="png" label="Plot at m/z=$mz_value and rt=$rt of $input.element_identifier"/>
38 </outputs> 43 </outputs>
39 <tests> 44 <tests>
40 <test> 45 <test>
41 <param name="input" value="xcms_plot_raw_testdata.mzML"/> 46 <param name="input" value="xcms_plot_raw_testdata.mzML"/>
42 <param name="mz_value" value="153.06583"/> 47 <param name="mz_value" value="153.06583"/>
43 <param name="tolerance_ppm" value="10"/> 48 <param name="tolerance_ppm" value="10"/>
44 <param name="rt" value="171.922"/> 49 <param name="rt" value="171.922"/>
45 <param name="rt_range" value="0.1"/> 50 <param name="rt_range" value="5"/>
46 <output name="output_filename" file="raw_plot.png" compare="sim_size" delta="5000"/> 51 <output name="output_filename">
52 <assert_contents>
53 <has_image_channels channels="3"/>
54 <has_image_center_of_mass center_of_mass="240.30, 240.51" eps="0.1"/>
55 </assert_contents>
56 </output>
47 </test> 57 </test>
48 </tests> 58 </tests>
49 <help><![CDATA[ 59 <help><![CDATA[
50 This tool plots the raw data filtered by m/z range and retention time (RT) range from an mzML file. 60 This tool plots the raw data filtered by m/z range and retention time (RT) range from an mzML file.
51 It uses a default tolerance of 10 ppm and retention time range of 5 s. 61 It uses a default tolerance of 10 ppm and retention time range of 5 s.