--- a/filetypes.txt	Fri May 17 09:59:52 2019 -0400
+++ b/filetypes.txt	Wed Sep 09 12:42:24 2020 +0000
@@ -1,29 +1,85 @@
-# CTD type    # Galaxy type     # Long Galaxy data type                    # Mimetype
-csv           tabular           galaxy.datatypes.tabular:Tabular
-fasta         fasta             galaxy.datatypes.sequence:Fasta
-FASTA         fasta             galaxy.datatypes.sequence:Fasta
-ini           txt               galaxy.datatypes.data:Text
-txt           txt               galaxy.datatypes.data:Text
-options       txt               galaxy.datatypes.data:Text
-grid          grid              galaxy.datatypes.data:Grid
-html          html              galaxy.datatypes.text:Html                  text/html
-HTML          html              galaxy.datatypes.text:Html                  text/html
-TraML         traml             galaxy.datatypes.proteomics:TraML           application/xml
-traML         traml             galaxy.datatypes.proteomics:TraML           application/xml
-XML           xml               galaxy.datatypes.xml:GenericXml             application/xml
-consensusXML  consensusxml      galaxy.datatypes.proteomics:ConsensusXML    application/xml
-edta          tabular           galaxy.datatypes.tabular:Tabular 
-featureXML    featurexml        galaxy.datatypes.proteomics:FeatureXML      application/xml
-idXML         idxml             galaxy.datatypes.proteomics:IdXML           application/xml
-mzML          mzml              galaxy.datatypes.proteomics:MzML            application/xml
-mzXML         mzxml             galaxy.datatypes.proteomics:MzXML           application/xml
-pepXML        pepxml            galaxy.datatypes.proteomics:PepXml          application/xml
-qcML          qcml              galaxy.datatypes.xml:GenericXml             application/xml
-trafoXML      trafoxml          galaxy.datatypes.xml:GenericXml             application/xml
-tsv           tabular           galaxy.datatypes.tabular:Tabular
-xsd           txt               galaxy.datatypes.data:Text
-mzq           mzq               galaxy.datatypes.proteomics:MzQuantML       application/xml
-msp           msp               galaxy.datatypes.proteomics:Msp
-mzid          mzid              galaxy.datatypes.proteomics:MzIdentML       application/xml
-png           png               galaxy.datatypes.images:Png                 image/png
-mgf           mgf               galaxy.datatypes.proteomics:Mgf
+# CTD type    # Galaxy type
+# the following lines need to be at the top in order to ensure 
+# correct translation Galaxy->CTD type for the ambiguous cases
+# (should only be relevant for the autogenerated tests [which 
+# do not set the ftype of the inputs])
+txt           txt
+tsv           tabular
+
+##analysisXML
+# XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters 
+bioml         xml
+consensusXML  consensusxml
+# TODO csv is problematic, since csv often actually means tsv .. but not always
+csv           csv
+##dat
+dta           dta
+dta2d         dta2d
+edta          edta
+fa            fasta
+fas           fasta
+fasta         fasta
+FASTA         fasta
+featureXML    featurexml
+featurexml    featurexml
+# fid
+html          html
+HTML          html
+idXML         idxml
+##ini         txt
+json          json
+kroenik	      kroenik
+mascotXML     mascotxml
+mgf           mgf
+mrm           mrm
+ms            sirius.ms
+ms2           ms2
+msp           msp
+mzData        mzdata
+mzid          mzid
+# important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444
+mzML          mzml
+mzml          mzml
+mzq           mzq
+mzTab         mztab
+mzXML         mzxml
+novor         txt
+obo           obo
+# I guess this is the idXML output of omssa
+omssaXML      idxml
+osw           osw
+OSW           osw
+params        txt
+paramXML      paramxml
+fasta         peff
+peplist       peplist
+# TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541
+pep.xml       pepxml
+pepXML        pepxml
+png           png
+PNG           png
+protXML       protxml
+psms          psms
+# TODO implement or use
+# psq
+pqp           pqp
+qcML          qcml
+spec.xml      spec.xml
+splib         splib
+sqMass        sqmass
+tandem.xml    tandem
+trafoXML      trafoxml
+traML         traml
+TraML         traml
+tab           tabular
+## MOVED TO TOP txt           txt
+raw           thermo.raw
+## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419
+xls           tsv
+XML           xml
+xml           xml
+xquest.xml    xquest.xml
+xsd           xml
+
+# TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml
+# cachedMzML    xml