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Commit message:
Improved readme |
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README.rst |
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README |
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| diff -r ac51d9dbfb4d -r de34893b3834 README --- a/README Tue Mar 24 23:46:23 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,11 +0,0 @@ -# What is it? - -Galaxy datatype and display-application definitions for Proteomics data - -# Installation - -Install into your local galaxy instance from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -˝To visualize data you will need to install the protviz visualization web application. This is available at -[https://bitbucket.org/Andrew_Brock/proteomics-visualise](https://bitbucket.org/Andrew_Brock/proteomics-visualise) - |
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| diff -r ac51d9dbfb4d -r de34893b3834 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun Mar 29 19:24:40 2015 -0400 |
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| @@ -0,0 +1,63 @@ +Proteomics Datatypes +==================== + +Support for a proteomics and mass spectrometry datatypes for Galaxy_ + +.. _Galaxy: http://galaxyproject.org/ + + +Included Datatypes +------------------ + +================ ===================== ======= ==================================== +Class Extension Sniffer Application or Purpose +================ ===================== ======= ==================================== +Binary cps False SearchGUI_ / PeptideShaker_ +PepXML_ raw_pepxml True TPP_ Search Engine Outputs +PepXML_ peptideprophet_pepxml True TPP_ PeptideProphet Outputs +PepXML_ interprophet_pepxml True TPP_ iProphet Outputs +ProtXML_ protxml True TPP_ ProteinProphet Outputs +GenericXML trafoxml False OpenMS_ RT Transforms +GenericXML qcml_ False OpenMS_ QC Data +PepXmlReport pepxml.tsv False Tabular PepXML +ProtXmlReport protxml.tsv False Tabular ProtXML +MascotDat mascotdat False Raw Mascot Search Results +MzML_ mzml True Raw Mass Spec Data +Mgf mgf True MS/MS Spectra +IdpDB idpdb False +Wiff wiff False Raw Mass Spec Data +MzXML mzxml True Raw Mass Spec Data +MzQuantML_ mzq True HUPO standard for quant data +MzIdentML_ mzid True HUPO standard for ID data +TraML_ traml True HUPO standard for transition lists +FeatureXML featurexml False OpenMS_ +ConsensusXML consensusxml False OpenMS_ +IdXML idxml False OpenMS_ +TandemXML_ tandem False XTandem output +RAW raw False Raw Mass Spec Data +Msp msp False Spectral Library +Ms2 ms2 False MS/MS Spectra +XHunterAslFormat hlf False Spectral Library +================ ===================== ======= ==================================== + + +.. _qcml: http://code.google.com/p/qcml +.. _PepXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML +.. _ProtXML: http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML +.. _TPP: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP +.. _OpenMS: https://github.com/OpenMS/OpenMS +.. _SearchGUI: https://code.google.com/p/searchgui/ +.. _PeptideShaker: https://code.google.com/p/peptide-shaker/ +.. _MzML: http://www.psidev.info/mzml_1_0_0%20 +.. _MzQuantML: http://www.psidev.info/mzquantml +.. _MzIdentML: http://www.psidev.info/mzidentml +.. _TraML: http://www.psidev.info/traml +.. _TandemXML: http://www.thegpm.org/docs/X_series_output_form.pdf + +Visualization +------------- + +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. + +.. _protviz: https://bitbucket.org/Andrew_Brock/proteomics-visualise + |