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workflow4metabolomics / tools-metabolomics

Galaxy tools for metabolomics maintained by Workflow4Metabolomics
https://workflow4metabolomics.org/
GNU General Public License v3.0
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xcmsSet , in file name #68

Closed bernt-matthias closed 6 years ago

bernt-matthias commented 7 years ago

If a file with a ',' in the file name is used as input then the link is not created properly (the name of the link is the prefix of the filename up to the comma) and xcms does not find input data:

Error in xcmsSet(".", nSlaves = 1, method = "centWave", ppm = 25, peakwidth = c(10,  : 
  No NetCDF/mzXML/mzData/mzML files were found.

Seems to be related to: https://github.com/workflow4metabolomics/xcms/issues/65 (some escaping seems to be necessary).

lecorguille commented 7 years ago

Oh a , in the filename. I never expected that :)

Are you using as input a 'single' file or a zip file?

bernt-matthias commented 7 years ago

Input is a single file. Actually I do not know the intension of the comma. One of our users just send me a bug report. I guess there is a float value encoded in the file name and germans use ',' instead of '.' in floats. I could ask if you are interested.

Input is a single file.

lecorguille commented 6 years ago

@bernt-matthias It should be fixed in the future wrappers for xcms3 https://github.com/workflow4metabolomics/xcms/pull/84/commits/1e6ed0300ba6105ac0236d04b66ae44d12851aeb