Mercurial > repos > galaxyp > openms_mascotadapter

comparison filetypes.txt @ 9:fb751f9c050b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:07:35 +0000
parents 36da1e3613ea
children 57fb2083a8cb
comparison
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8:e52d5d3bfc62 9:fb751f9c050b
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