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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author galaxyp
date Thu, 24 Sep 2020 12:26:30 +0000
parents 4f8478024146
children f8475273db10
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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

##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