Mercurial > repos > iracooke > proteomics_datatypes
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| author | iracooke |
|---|---|
| date | Thu, 04 Jun 2015 08:10:37 -0400 |
| parents | d1ea609e57d4 |
| children |
| rev | line source |
|---|---|
| 15 | 1 Proteomics Datatypes |
| 2 ==================== | |
| 3 | |
| 4 Support for a proteomics and mass spectrometry datatypes for Galaxy_ | |
| 5 | |
| 6 .. _Galaxy: http://galaxyproject.org/ | |
| 7 | |
| 8 | |
| 9 Included Datatypes | |
| 10 ------------------ | |
| 11 | |
| 12 ================ ===================== ======= ==================================== | |
| 13 Class Extension Sniffer Application or Purpose | |
| 14 ================ ===================== ======= ==================================== | |
| 15 Binary cps False SearchGUI_ / PeptideShaker_ | |
| 16 PepXML_ raw_pepxml True TPP_ Search Engine Outputs | |
| 17 PepXML_ peptideprophet_pepxml True TPP_ PeptideProphet Outputs | |
| 18 PepXML_ interprophet_pepxml True TPP_ iProphet Outputs | |
| 19 ProtXML_ protxml True TPP_ ProteinProphet Outputs | |
| 20 GenericXML trafoxml False OpenMS_ RT Transforms | |
| 21 GenericXML qcml_ False OpenMS_ QC Data | |
| 22 PepXmlReport pepxml.tsv False Tabular PepXML | |
| 23 ProtXmlReport protxml.tsv False Tabular ProtXML | |
| 24 MascotDat mascotdat False Raw Mascot Search Results | |
| 25 MzML_ mzml True Raw Mass Spec Data | |
| 26 Mgf mgf True MS/MS Spectra | |
| 27 IdpDB idpdb False | |
| 28 Wiff wiff False Raw Mass Spec Data | |
| 29 MzXML mzxml True Raw Mass Spec Data | |
| 30 MzQuantML_ mzq True HUPO standard for quant data | |
| 31 MzIdentML_ mzid True HUPO standard for ID data | |
| 32 TraML_ traml True HUPO standard for transition lists | |
| 33 FeatureXML featurexml False OpenMS_ | |
| 34 ConsensusXML consensusxml False OpenMS_ | |
| 35 IdXML idxml False OpenMS_ | |
| 36 TandemXML_ tandem False XTandem output | |
| 37 RAW raw False Raw Mass Spec Data | |
| 17 | 38 Msp_ msp True Spectral Library |
| 18 | 39 SPLib_ splib True Spectral Library |
| 15 | 40 Ms2 ms2 False MS/MS Spectra |
| 41 XHunterAslFormat hlf False Spectral Library | |
| 42 ================ ===================== ======= ==================================== | |
| 43 | |
| 44 | |
| 45 .. _qcml: http://code.google.com/p/qcml | |
| 46 .. _PepXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML | |
| 47 .. _ProtXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML | |
| 48 .. _TPP: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP | |
| 49 .. _OpenMS: https://github.com/OpenMS/OpenMS | |
| 50 .. _SearchGUI: https://code.google.com/p/searchgui/ | |
| 51 .. _PeptideShaker: https://code.google.com/p/peptide-shaker/ | |
| 52 .. _MzML: http://www.psidev.info/mzml_1_0_0%20 | |
| 53 .. _MzQuantML: http://www.psidev.info/mzquantml | |
| 54 .. _MzIdentML: http://www.psidev.info/mzidentml | |
| 55 .. _TraML: http://www.psidev.info/traml | |
| 56 .. _TandemXML: http://www.thegpm.org/docs/X_series_output_form.pdf | |
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e6a02a387448
planemo upload commit 4f23896d1a519a87f189c6238a95b8f5b5933e9a-dirty
iracooke
parents:
15
diff
changeset
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57 .. _Msp: http://chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf |
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e6a02a387448
planemo upload commit 4f23896d1a519a87f189c6238a95b8f5b5933e9a-dirty
iracooke
parents:
15
diff
changeset
|
58 .. _SPLib: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST#Developer.27s_Guide |
| 15 | 59 |
| 60 Visualization | |
| 61 ------------- | |
| 62 | |
| 63 This package also installs display applications for mzML, PepXML and ProtXML formats. These are designed to work with the protviz_ web application. Configuring this application requires a fair number of extra steps though. See the protviz_ documentation for more info. | |
| 64 | |
| 65 .. _protviz: https://bitbucket.org/Andrew_Brock/proteomics-visualise | |
| 66 |