The tool should visualize the extracted ion chromatogram (EIC) given a single mzml file (in a first step), the MZ value at which to extract the slice and the tolerance to use for extraction.
XCMS is already as a package in bioconda via bioconductor, same as Spectra and MetaboCoreUtils, they can therefore be specified as a requirement in the galaxy tool if they are needed.
In a next step, it would be great if the tool also worked on a collection and it would be possible to add a legend with the sample names and different colors for the samples. This could then also be extended towards the formats that mzR/XCMS/Spectra can handle, meaning mzData, mzxml and raw.
Another option for extension would be to implement something similar like is done here with rawRR to plot multiple EICs of a single sample in a single plot.
TLDR
[x] tool which runs on mzml and gives an EIC as PNG
[ ] rename the output to eic at <mz> of <dataset id>
[ ] update the help text
[ ] add reference to jo rainers tutorial (once on zenodo)
The tool should visualize the extracted ion chromatogram (EIC) given a single mzml file (in a first step), the MZ value at which to extract the slice and the tolerance to use for extraction.
The documentation for the R packages which should be used for these operations is here: https://jorainer.github.io/xcmsTutorials/articles/xcms-preprocessing.html#data-visualization This also includes a tutorial of how to call the functions as well as example outputs.
XCMS is already as a package in bioconda via bioconductor, same as
SpectraandMetaboCoreUtils, they can therefore be specified as a requirement in the galaxy tool if they are needed.In a next step, it would be great if the tool also worked on a collection and it would be possible to add a legend with the sample names and different colors for the samples. This could then also be extended towards the formats that mzR/XCMS/Spectra can handle, meaning
mzData,mzxmlandraw.Another option for extension would be to implement something similar like is done here with rawRR to plot multiple EICs of a single sample in a single plot.
TLDR
eic at <mz> of <dataset id>