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ISA-tools / mzml2isa

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure
GNU General Public License v3.0
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Second a_assay is missing instrument #27

Closed sneumann closed 7 years ago

sneumann commented 7 years ago

Hi, I have a study with pos and neg mzML files, and the second assay seems to be missing the Platform: image

and indeed, Study Assay Technology Platform is only written out for the first assay:

STUDY ASSAYS
Study Assay File Name   "a_MTBLSX_POS_metabolite_profiling_mass_spectrometry.txt"   "a_MTBLSX_NEG_metabolite_profiling_mass_spectrometry.txt"
Study Assay Measurement Type    "metabolite profiling"  "metabolite profiling"
Study Assay Measurement Type Term Accession Number  "http://purl.obolibrary.org/obo/OBI_0000366"    "http://purl.obolibrary.org/obo/OBI_0000366"
Study Assay Measurement Type Term Source REF    "OBI"   "OBI"
Study Assay Technology Type "mass spectrometry" "mass spectrometry"
Study Assay Technology Type Term Accession Number   "http://purl.obolibrary.org/obo/OBI_0000470"    "http://purl.obolibrary.org/obo/OBI_0000470"
Study Assay Technology Type Term Source REF "OBI"   "OBI"
Study Assay Technology Platform "micrOTOF-Q"

Yours, Steffen

Tomnl commented 7 years ago

Hi Steffen,

Thanks for finding this. It seems the "Study" template is not setup correctly to handle this situation.

I will look into this.

Cheers, Tom

rsalek commented 7 years ago

Thx

Tomnl commented 7 years ago

This issue should be fixed now see #28