Mercurial > repos > galaxyp > openms_ffeval
diff filetypes.txt @ 11:12513e823fd0 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 20:08:15 +0000 |
| parents | c0773af96cb8 |
| children | a02af506fe40 |
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--- a/filetypes.txt Fri May 17 09:52:06 2019 -0400 +++ b/filetypes.txt Wed Sep 09 20:08:15 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