Mercurial > repos > galaxyp > openms_idfileconverter
comparison filetypes.txt @ 11:43a1db77b7a6 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 12:55:15 +0000 |
| parents | 066cf4d993f5 |
| children | 250d6a43f66b |
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| 10:3baeecbd6e0f | 11:43a1db77b7a6 |
|---|---|
| 1 # CTD type # Galaxy type # Long Galaxy data type # Mimetype | 1 # CTD type # Galaxy type |
| 2 csv tabular galaxy.datatypes.tabular:Tabular | 2 # the following lines need to be at the top in order to ensure |
| 3 fasta fasta galaxy.datatypes.sequence:Fasta | 3 # correct translation Galaxy->CTD type for the ambiguous cases |
| 4 FASTA fasta galaxy.datatypes.sequence:Fasta | 4 # (should only be relevant for the autogenerated tests [which |
| 5 ini txt galaxy.datatypes.data:Text | 5 # do not set the ftype of the inputs]) |
| 6 txt txt galaxy.datatypes.data:Text | 6 txt txt |
| 7 options txt galaxy.datatypes.data:Text | 7 tsv tabular |
| 8 grid grid galaxy.datatypes.data:Grid | 8 |
| 9 html html galaxy.datatypes.text:Html text/html | 9 ##analysisXML |
| 10 HTML html galaxy.datatypes.text:Html text/html | 10 # XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters |
| 11 TraML traml galaxy.datatypes.proteomics:TraML application/xml | 11 bioml xml |
| 12 traML traml galaxy.datatypes.proteomics:TraML application/xml | 12 consensusXML consensusxml |
| 13 XML xml galaxy.datatypes.xml:GenericXml application/xml | 13 # TODO csv is problematic, since csv often actually means tsv .. but not always |
| 14 consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml | 14 csv csv |
| 15 edta tabular galaxy.datatypes.tabular:Tabular | 15 ##dat |
| 16 featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml | 16 dta dta |
| 17 idXML idxml galaxy.datatypes.proteomics:IdXML application/xml | 17 dta2d dta2d |
| 18 mzML mzml galaxy.datatypes.proteomics:MzML application/xml | 18 edta edta |
| 19 mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml | 19 fa fasta |
| 20 pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml | 20 fas fasta |
| 21 qcML qcml galaxy.datatypes.xml:GenericXml application/xml | 21 fasta fasta |
| 22 trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml | 22 FASTA fasta |
| 23 tsv tabular galaxy.datatypes.tabular:Tabular | 23 featureXML featurexml |
| 24 xsd txt galaxy.datatypes.data:Text | 24 featurexml featurexml |
| 25 mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml | 25 # fid |
| 26 msp msp galaxy.datatypes.proteomics:Msp | 26 html html |
| 27 mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml | 27 HTML html |
| 28 png png galaxy.datatypes.images:Png image/png | 28 idXML idxml |
| 29 mgf mgf galaxy.datatypes.proteomics:Mgf | 29 ##ini txt |
| 30 json json | |
| 31 kroenik kroenik | |
| 32 mascotXML mascotxml | |
| 33 mgf mgf | |
| 34 mrm mrm | |
| 35 ms sirius.ms | |
| 36 ms2 ms2 | |
| 37 msp msp | |
| 38 mzData mzdata | |
| 39 mzid mzid | |
| 40 # important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444 | |
| 41 mzML mzml | |
| 42 mzml mzml | |
| 43 mzq mzq | |
| 44 mzTab mztab | |
| 45 mzXML mzxml | |
| 46 novor txt | |
| 47 obo obo | |
| 48 # I guess this is the idXML output of omssa | |
| 49 omssaXML idxml | |
| 50 osw osw | |
| 51 OSW osw | |
| 52 params txt | |
| 53 paramXML paramxml | |
| 54 fasta peff | |
| 55 peplist peplist | |
| 56 # TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541 | |
| 57 pep.xml pepxml | |
| 58 pepXML pepxml | |
| 59 png png | |
| 60 PNG png | |
| 61 protXML protxml | |
| 62 psms psms | |
| 63 # TODO implement or use | |
| 64 # psq | |
| 65 pqp pqp | |
| 66 qcML qcml | |
| 67 spec.xml spec.xml | |
| 68 splib splib | |
| 69 sqMass sqmass | |
| 70 tandem.xml tandem | |
| 71 trafoXML trafoxml | |
| 72 traML traml | |
| 73 TraML traml | |
| 74 tab tabular | |
| 75 ## MOVED TO TOP txt txt | |
| 76 raw thermo.raw | |
| 77 ## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419 | |
| 78 xls tsv | |
| 79 XML xml | |
| 80 xml xml | |
| 81 xquest.xml xquest.xml | |
| 82 xsd xml | |
| 83 | |
| 84 # TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml | |
| 85 # cachedMzML xml |