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Run xcmsSet on each input file individually #2
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We will be able to carry on new developments since planemo shed_test for all tools in this repo |
Let's go! |
In progress: #13 |
Available from the testtoolshed since the version 2.1.0 The CAMERA part will fail. I'm working on that workflow4metabolomics/camera.archive#15 |
Available within the dev galaxy instance |
Unfortunatly, we can't currently import CDF file in the dev instance because it need to be updated.
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Can't manage to make the merge work:
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Need more debugging information. The warning is from package mzR and Rcpp, |
@melpetera I observed this behaviour when I merge MM8 and MM14 obtained with the default parameters of xcmsSet.
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Oh right! I didn't notice... I'll try to change my initial xcmsSet parameters. |
Meanwhile, I should raise and error because currently this kind of result is green |
Now that my xcmsSet output files are good, the whole workflow works perfectly! |
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. <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. |
Pong: @bgruening |
ping! :) Stupid question what happens if in the zip are 10 files? |
Done: #44 Available within the dev galaxy instance |
@yguitton |
Tested on dev galaxy instance:
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Cool! What is the link to the dev galaxy instance ? |
OK for xcmSet Note still accent issue if some are present inside mzXML files |
@sneumann The URL is https://galaxydev.workflow4metabolomics.org |
Validated 👍 |
To really close this thread Here is a little screencast about how to run in parallel xcmsSet within W4M using single files [link] |
Sorry for the delay. |
Add Metabolomics tag in Galaxy toolshed descriptions.
genform: remove help from test param
Then Galaxy can parallelize the execution.
For backwards compatibility, check at
https://github.com/workflow4metabolomics/xcms/blob/master/src/xcms_w4m_script/xcms.r#L122
if a ZIP or an mzML/netCDF/... is provided.
Then you get one xcmsSet per input file.
After all N xcmsSets are created, use " c(xs1, xs2, xs3, ..." to combine
all individual xcmsSets into one big, like the existing node does.
Yours, Steffen
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