Mercurial > repos > workflow4metabolomics > xcms_plot_raw

annotate xcms_plot_raw.xml @ 1:8b8d360316c3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
1 <tool id="xcms_plot_raw" name="xcms plot raw" version="@TOOL_VERSION@+galaxy0" profile="21.09">
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
2 <description>Plot raw data filtered by m/z range and retention time (RT) range</description>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
3 <macros>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
4 <import>macros_xcms_plot.xml</import>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
5 </macros>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
6 <expand macro="bio.tools"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
7 <expand macro="creator"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
8 <requirements>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
10 </requirements>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
12 Rscript -e 'source("${plot_raw}")'
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
13 ]]></command>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
14 <configfiles>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
15 <configfile name="plot_raw">
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
16 library(xcms)
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
17 library(MsExperiment)
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
18 library(Spectra)
1
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
19
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
20 sessionInfo()
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
21
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
22 mse = readMsExperiment(file.path('${input}'))
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
23 mz_offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
1
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
24 rt_offset = ${rt_range}
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
25
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
26 raw = mse |>
1
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
27 filterMsLevel(msLevel = ${mslevel}L) |>
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
28 filterRt(rt = ${rt} + c(-rt_offset, rt_offset)) |>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
29 filterMzRange(mz = ${mz_value} + c(-mz_offset, mz_offset))
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
30 png(filename = '${output_filename}')
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
31 par(oma = c(0.5, 2, 0.5, 1))
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
32 plot(raw)
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
33 dev.off()
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
34 </configfile>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
35 </configfiles>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
36 <inputs>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
37 <expand macro="base_params"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
38 <param type="float" name="rt" label="Retention Time" min="0.0" value="0.0" help="Retention time for the plot"/>
1
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
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 (+-)."/>
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
40 </inputs>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
41 <outputs>
1
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
42 <data name="output_filename" format="png" label="Plot at m/z=$mz_value and rt=$rt of $input.element_identifier"/>
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
43 </outputs>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
44 <tests>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
45 <test>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
46 <param name="input" value="xcms_plot_raw_testdata.mzML"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
47 <param name="mz_value" value="153.06583"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
48 <param name="tolerance_ppm" value="10"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
49 <param name="rt" value="171.922"/>
1
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
50 <param name="rt_range" value="5"/>
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
51 <output name="output_filename">
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
52 <assert_contents>
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
53 <has_image_channels channels="3"/>
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
54 <has_image_center_of_mass center_of_mass="240.30, 240.51" eps="0.1"/>
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
55 </assert_contents>
8b8d360316c3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f
workflow4metabolomics
parents: 0
diff changeset
56 </output>
0
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
57 </test>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
58 </tests>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
59 <help><![CDATA[
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
60 This tool plots the raw data filtered by m/z range and retention time (RT) range from an mzML file.
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
61 It uses a default tolerance of 10 ppm and retention time range of 5 s.
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
62 More information and detailed instructions can be found in the tutorial at: https://jorainer.github.io/xcmsTutorials/articles/xcms-preprocessing.html#data-visualization
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
63 ]]></help>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
64 <expand macro="citations"/>
520448a32548 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
workflow4metabolomics
parents:
diff changeset
65 </tool>