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XCMS tools for plotting EIC and Peaks #523

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XCMS tools for plotting EIC and Peaks #523

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wverastegui
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@wverastegui wverastegui commented Apr 23, 2024

This PR contains the XCMS plotting tools for peaks and EIC.

  • Updated the help text
  • Updated the test for mzML
  • Renamed outputname, it inlcudes <m/z>, and <dataset_id>
  • Fixed plot cutoff of the image
  • Updated test plots

closes #498 & #499

@wverastegui wverastegui requested a review from hechth April 23, 2024 07:45
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This commit fixed the issue of the left margin cutoff.

@hechth hechth marked this pull request as ready for review April 23, 2024 14:55
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Please see the comments and re-request review from me and @KristinaGomoryova after adressing them.

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wverastegui and others added 4 commits April 23, 2024 17:36
Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
Co-authored-by: Helge Hecht <helge.hecht@recetox.muni.cz>
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hechth commented Apr 23, 2024

@yguitton should we put those tools rather to the other w4m XCMS tools into your repo, what do you think?
@jorainer these tools add some of the plotting capabilities described in your XCMS tutorial to Galaxy. If you make it referenceable we can link it here so that people see the further functions provided by the package :)

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@yguitton should we put those tools rather to the other w4m XCMS tools into your repo, what do you think?
@hechth Yes we should add that to W4M, as it really fits our users needs

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hechth commented Apr 24, 2024

@yguitton then I will close this here and open a new PR on w4m - should we make a new folder for these like xcms_plot or put them to the existing folder?

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Implement a tool to plot the EIC given a mass using XCMS
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