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Added XCMS plotting tools #267

Merged
merged 8 commits into from
Jul 15, 2024
Merged

Added XCMS plotting tools #267

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c00c68f
initial commit
hechth Apr 29, 2024
4adb9a4
merged with xcms folder
hechth Apr 29, 2024
48c39d0
switched to other macro file
hechth May 9, 2024
7ba4b3b
fixed indentation
hechth May 9, 2024
09d7c48
Update tools/xcms/xcms_plot_raw.xml
bgruening May 13, 2024
5dbf760
added reference to jo rainers tutorials
hechth May 21, 2024
67fa2b3
Merge branch 'xcms_plot' of github.com:hechth/tools-metabolomics into…
hechth May 21, 2024
1f13c9b
fixed test
zargham-ahmad Jul 15, 2024
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35 changes: 34 additions & 1 deletion tools/xcms/.shed.yml
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Expand Up @@ -111,7 +111,38 @@ repositories:
owner: lecorguille
include:
[*default-includes, msnbase_readmsdata.xml, msnbase_readmsdata.r, macros_msnbase.xml]

xcms_plot_raw:
description: Plot raw mzml file content with xcms
long_description: |
This suite provides tools from the XCMS package to visualize extracted ion chromatograms and raw data
from a single mzML file. Users can define m/z and retention time (rt) values, and the suite plots data
with a user-defined tolerance and rt range centered around the selected m/z and rt values.
The MsExperiment plot function creates a two-dimensional view of three-dimensional mass spectrometry data,
displaying peaks in the two-dimensional m/z versus retention time plane with intensity color-coding. The plot
is saved as a PNG file
owner: workflow4metabolomics
type: unrestricted
include:
- xcms_plot_raw.xml
- macros_xcms_plot.xml
- test-data/raw_plot.png
- test-data/xcms_plot_raw_testdata.mzML
xcms_plot_eic:
description: Plot EIC using xcms
long_description: |
This suite provides tools from the XCMS package to visualize extracted ion chromatograms and raw data
from a single mzML file. Users can define m/z and retention time (rt) values, and the suite plots data
with a user-defined tolerance and rt range centered around the selected m/z and rt values.
The MsExperiment plot function creates a two-dimensional view of three-dimensional mass spectrometry data,
displaying peaks in the two-dimensional m/z versus retention time plane with intensity color-coding. The plot
is saved as a PNG file
owner: workflow4metabolomics
type: unrestricted
include:
- xcms_plot_eic.xml
- macros_xcms_plot.xml
- test-data/eic_plot.png
- test-data/xcms_plot_eic_testdata.mzML
suite:
name: suite_xcms
owner: lecorguille
Expand All @@ -122,3 +153,5 @@ suite:
http://www.bioconductor.org/packages/release/bioc/html/xcms.html
XCMS: processing mass spectrometry data for metabolite profiling
using nonlinear peak alignment, matching, and identification


38 changes: 38 additions & 0 deletions tools/xcms/macros_xcms_plot.xml
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@@ -0,0 +1,38 @@
<macros>
<token name="@TOOL_VERSION@">4.0.0</token>
<xml name="creator">
<creator>
<person
givenName="Wudmir"
familyName="Rojas"
url="https://github.com/wverastegui"
identifier="0000-0001-7036-9987" />
<person
givenName="Helge"
familyName="Hecht"
url="https://github.com/hechth"
identifier="0000-0001-6744-996X" />
<organization
url="https://www.recetox.muni.cz/"
email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
name="RECETOX MUNI"/>
</creator>
</xml>
<xml name="bio.tools">
<xrefs>
<xref type="bio.tools">XCMS</xref>
</xrefs>
</xml>
<xml name="base_params">
<param type="data" name="input" format="mzML" label="Input mzML file"/>
<param type="float" name="mz_value" value="10.0" min="0.0" label="m/z Value" help="m/z value for the EIC"/>
<param type="integer" value="10" name="tolerance_ppm" min="0" label="Tolerance (ppm)" help="Tolerance for m/z value in ppm"/>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1021/ac051437y</citation>
<citation type="doi">10.3390/metabo12020173</citation>
<citation type="doi">10.5281/zenodo.11185520</citation>
</citations>
</xml>
</macros>
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3,801 changes: 3,801 additions & 0 deletions tools/xcms/test-data/xcms_plot_eic_testdata.mzML
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212 changes: 212 additions & 0 deletions tools/xcms/test-data/xcms_plot_raw_testdata.mzML
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