# HG changeset patch
# User iracooke
# Date 1427671480 14400
# Node ID de34893b3834df134cbe1b6f77bf4dc9dbdcecff
# Parent  ac51d9dbfb4db49a506e1023928c4ad6269e892c
Improved readme

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
@@ -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)
-
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
@@ -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
+