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new data types for OpenMS #8109
Merged
jmchilton
merged 29 commits into
galaxyproject:dev
from
bernt-matthias:topic/openms-datatypes
Apr 20, 2020
Merged
new data types for OpenMS #8109
jmchilton
merged 29 commits into
galaxyproject:dev
from
bernt-matthias:topic/openms-datatypes
Apr 20, 2020
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And search root tag not only at the beginning of the line, i.e. and switch pattern '^<(\w*:)?ROOT' to '<(\w*:)?ROOT' and search instead of match ("^" in combination with match was not necessary anyway).
- no sniffing for dta - remove superficial len checks - schema links to OpenMS with commit
as subclass of text
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Hi @bgruening except for datatypes derived from ProteomicsXml all new data types have now working working doc-tests. I'm hesitant (aka. lazy) to add doc-tests for the ProteomicsXml cases .. what do you think? |
bgruening
approved these changes
Apr 10, 2020
This PR was merged without a 'kind/' tag, please correct. |
Wuhu! Thanks for the merge @jmchilton! |
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Needed here galaxyproteomics/tools-galaxyp#266
dta
,dta2d
,edta
dta
: 2 column space separated float/int? https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/a09160.htmledta
in the examples I found tabular data with inconsistent headersRT mz Int charge Meta2
,RT MZ INT CHARGE rt1 mz1 int1 charge1 Rt2 Mz2 Int2 Charge2 rT3 mZ3 inT3 chargE3
dta2d
3 column float/int https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/a09156.htmlmascotxml
mztab
mzTab
(v1.x designed for proteomics) https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/1_0-Proteomics-Release/mzTab_format_specification.pdfmzTab-M
(= v2.x mzTab) https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#relationship-to-mztab-1.0pqp
andosw
PQP file definition OpenMS/OpenMS#4365CHROMATOGRAM PRECURSOR RUN SPECTRUM DATA PRODUCT RUN_EXTRA
trafoXML
xquest.xml
Maybe useful https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/