Mercurial > repos > galaxyp > openms_rnpxlsearch

annotate filetypes.txt @ 7:7911914e96f6 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 19:56:16 +0000
parents c6911370f25e
children 3dc6d9795d5b
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7
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 # CTD type # Galaxy type
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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2 # the following lines need to be at the top in order to ensure
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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3 # correct translation Galaxy->CTD type for the ambiguous cases
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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4 # (should only be relevant for the autogenerated tests [which
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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5 # do not set the ftype of the inputs])
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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6 txt txt
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7 tsv tabular
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8
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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9 ##analysisXML
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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10 # XTandemAdapter output is named xml in OMS (which is to unspecific) and bioml in Galaxy .. so this is renamed via hardcoded parameters
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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11 bioml xml
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12 consensusXML consensusxml
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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13 # TODO csv is problematic, since csv often actually means tsv .. but not always
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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14 csv csv
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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15 ##dat
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16 dta dta
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17 dta2d dta2d
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18 edta edta
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19 fa fasta
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20 fas fasta
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21 fasta fasta
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22 FASTA fasta
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23 featureXML featurexml
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24 featurexml featurexml
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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25 # fid
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26 html html
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27 HTML html
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28 idXML idxml
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29 ##ini txt
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30 json json
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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31 kroenik kroenik
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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32 mascotXML mascotxml
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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33 mgf mgf
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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34 mrm mrm
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35 ms sirius.ms
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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36 ms2 ms2
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37 msp msp
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38 mzData mzdata
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39 mzid mzid
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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40 # important to have mzML first, since LuciphorAdapter is case sensitive https://github.com/OpenMS/OpenMS/issues/4444
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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41 mzML mzml
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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42 mzml mzml
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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43 mzq mzq
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44 mzTab mztab
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45 mzXML mzxml
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46 novor txt
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47 obo obo
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48 # I guess this is the idXML output of omssa
7911914e96f6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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49 omssaXML idxml
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50 osw osw
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51 OSW osw
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52 params txt
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53 paramXML paramxml
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54 fasta peff
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55 peplist peplist
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56 # TODO pep.xml should be removed with OMS 2.6 https://github.com/OpenMS/OpenMS/pull/4541
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57 pep.xml pepxml
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58 pepXML pepxml
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59 png png
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60 PNG png
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61 protXML protxml
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62 psms psms
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63 # TODO implement or use
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64 # psq
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65 pqp pqp
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66 qcML qcml
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67 spec.xml spec.xml
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68 splib splib
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69 sqMass sqmass
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70 tandem.xml tandem
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71 trafoXML trafoxml
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72 traML traml
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73 TraML traml
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74 tab tabular
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75 ## MOVED TO TOP txt txt
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76 raw thermo.raw
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77 ## xls: SpectraSTSearchAdapter https://github.com/OpenMS/OpenMS/pull/4419
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78 xls tsv
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79 XML xml
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80 xml xml
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81 xquest.xml xquest.xml
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82 xsd xml
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83
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84 # TODO needs to be implemented, needs to be below xml in order that Galaxy->OMS mapping gives xml
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85 # cachedMzML xml