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PRIDE-Archive / px-submission-tool

ProteomeXchange data submission tool
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Directory-based MS data formats #107

Closed chambm closed 2 years ago

chambm commented 4 years ago

A user asked me how to convert some BAF files from a PRIDE dataset (PXD010092), and after investigating I had to tell them it's not possible because the dataset only included BAF files instead of the entire .d directory for each run, which is required for the Bruker Baf2Sql API to read the data. Similar to requiring .wiff.scan files for .wiff files when they are present, a user should not be allowed to upload BAF, YEP, and Waters RAW files as mere files. Either the upload tool has to support uploading the intact .d directories, or it needs to handle the directory as zipped or tar'd.

selvaebi commented 3 years ago

@ypriverol should we add this check ?

ypriverol commented 3 years ago

Yes

On Wed, May 5, 2021 at 11:10 AM Selvakumar Kamatchinathan < @.***> wrote:

@ypriverol https://github.com/ypriverol should we add this check ?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PRIDE-Archive/px-submission-tool/issues/107#issuecomment-832572508, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMXEKK5R2TYSCT7D4ARG3TMEKR5ANCNFSM4SGS54UQ .

-- Yasset Perez-Riverol PhD. Team Coordinator Proteomics Services European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK Twitter: @ypriverol

selvaebi commented 3 years ago

hi, @chambm Can you please give us an example .d directory and also let us know what is Waters' raw file extension. we only have 3 "baf","fid","yep"

chambm commented 3 years ago

There are many test files (Thermo RAW, Waters RAW, Bruker BAF, Agilent MassHunter, Sciex WIFF+SCAN) at: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert/test-data

Waters is MassLynxTest.raw.tar.