view filetypes.txt @ 13:31bc4129f589 draft

"planemo upload for repository commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:32:01 +0000
parents 65be0674bb70
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# 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

# 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
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
ms2           ms2
msp           msp
mzData        mzdata
mzid          mzid
# important to have mzML first, since LuciphorAdapter is case sensitive
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 .. but still in the tests
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
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