Comments (25)
To really close this thread
Here is a little screencast about how to run in parallel xcmsSet within W4M using single files [link]
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We will be able to carry on new developments since planemo shed_test for all tools in this repo
#3
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Let's go!
#13
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In progress: #13
Need to be tested
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Available from the testtoolshed since the version 2.1.0
docker run -d -p 8080:80 quay.io/workflow4metabolomics/galaxy-workflow4metabolomics:beta
The CAMERA part will fail. I'm working on that workflow4metabolomics/camera.archive#15
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Available within the dev galaxy instance
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Unfortunatly, we can't currently import CDF file in the dev instance because it need to be updated.
By can you try with some other format to:
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launch as many xcmsSet as input file
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merge the rdata with xcms.merger
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launch the whole workflow until camera
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validated by @melpetera
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validated by @yguitton
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validated by @jfrancoismartin
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validated by @pierrickrogermele
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Can't manage to make the merge work:
Tool execution generated the following error message:
Fatal error: Exit code 1 () Warning message: 'loadRcppModules' is deprecated. Use 'loadModule' instead. See help("Deprecated") Error in peaklist[[i]][, "sample"] : subscript out of bounds Calls: c -> c.xcmsSet Execution halted
The tool produced the following additional output:
XSET MERGING... QC_1 QC_2
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Need more debugging information. The warning is from package mzR and Rcpp,
but should (?!) still work. If not, I need to add a sanity check to c.xcmsSet().
In which R file is this c(xs1, xs2, ...) called ?
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@melpetera I observed this behaviour when I merge MM8 and MM14 obtained with the default parameters of xcmsSet.
I got this kind of xset:
XSET OBJECT INFO
An "xcmsSet" object with 1 samples
Time range: Inf--Inf seconds (Inf--Inf minutes)
Mass range: Inf--Inf m/z
Peaks: 0 (about 0 per sample)
Peak Groups: 0
Sample classes: .
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Oh right! I didn't notice... I'll try to change my initial xcmsSet parameters.
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Meanwhile, I should raise and error because currently this kind of result is green
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Now that my xcmsSet output files are good, the whole workflow works perfectly!
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ping at least @melpetera @yguitton
After some nocturnal reflections, I think I should simplified the form around the inputs.
Currently:
<conditional name="inputs">
<param name="input" type="select" label="Choose your inputs method" >
<option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
<option value="single_file">mzXML file from your history</option>
</param>
<when value="zip_file">
<param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
</when>
<when value="single_file">
<param name="single_file" type="data" format="mzxml,netcdf" label="Single file" />
</when>
</conditional>
So users have to choose the input method between zip_file or single_file (mzxml, ...) and then to select their input in their history.
What do you think about accept in the same param both zip file and individual files?
<param name="file" type="data" format="no_unzip.zip,zip,mzxml,mzml,netcdf,mzdata" label="Single file" />
If you agree with that, unfortunatly, at some point, I will ask you to test again the whole workflow.
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Pong: @bgruening
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ping! :)
I'm definitely in favor of the single input without a choice. So that you put everything in one format attribute. This should be a much better UX and less code :)
In a long run I would even try to remove the zip from the supported file types.
Stupid question what happens if in the zip are 10 files?
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Done: #44
Available within the dev galaxy instance
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@yguitton
The datatype netCDF and mzData are now supported within the galaxydev instance
Try again! :)
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Tested on dev galaxy instance:
- single input without a choice
- Run xcmsSet on each input file individually
- xcms.xcmsSet Merger
- reaching fillPeaks from individual input files
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Cool! What is the link to the dev galaxy instance ?
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OK for xcmSet
OK single and multiple mzXML
OK for single & multiple CDF in a zip
OK for single & multiple mzData in a zip
Note still accent issue if some are present inside mzXML files
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@sneumann The URL is https://galaxydev.workflow4metabolomics.org
If you have trouble to login, let me know :)
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Validated 👍
Thanks to my testers
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Sorry for the delay.
I made some mistakes in my tests...
Everything is ok for me now.
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Related Issues (20)
- readMSData error HOT 8
- suite_xcms not up to date
- xcms_chrom_plot missing color in group plot HOT 2
- Tools with picture issues in help section
- [xcms process history] error HOT 3
- findChromPeaks Merger with "bad " samplenames format auto correction HOT 1
- Please wrap the XCMS refineChromPeaks tool HOT 15
- AdjustRtime module : bug in wrapper
- camera_combinexsannos for EU Server installation
- Error when linking Isocor and Isoplot in a workflow HOT 8
- Metabolite correlation analysis - handling differences in order between tables
- xcmsSet - old version (rev: 15646e937936) - conda version resolving never finishes HOT 5
- xcms plot chromatogram - manage SampleMetadata with ad without X (check.names)
- Tool request: MZMine HOT 10
- fillPeaks function enhancement ChromPeakAreaParam
- test issue HOT 1
- metams: exchange MSP reader with MSBackendMSP from RforMassSpectrometry HOT 1
- Biocontainer not letting tool create subdirectory HOT 3
- Add DIMet tool in workflow4metabolomics
- Added tool Skyline2Isocor not being integrated onto W4M galaxy UI HOT 2
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