new data types for OpenMS #8109
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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. |
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Wuhu! Thanks for the merge @jmchilton! |
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Needed here galaxyproteomics/tools-galaxyp#266
dta,dta2d,edtadta: 2 column space separated float/int? https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/a09160.htmledtain 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 chargE3dta2d3 column float/int https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/a09156.htmlmascotxmlmztabmzTab(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-1.0pqpandoswPQP file definition OpenMS/OpenMS#4365CHROMATOGRAM PRECURSOR RUN SPECTRUM DATA PRODUCT RUN_EXTRAtrafoXMLxquest.xmlMaybe useful https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518119/