Mise à jour Doc, correction du jnlp pour inclure Mac OS X

git-svn-id: https://subversion.renater.fr/xtandempipeline/trunk@99 b8ef2a07-7df7-436f-90b9-41648038564b

xtandempipeline/doc/xtandem_pipeline.tex

@@ -9,18 +9,18 @@
 \usepackage{fancyhdr}
 \usepackage{geometry}
 
-\newcommand{\X}{\textbf{X!Tandem pipeline}}
+\newcommand{\X}{\textbf{X!Tandem Pipeline}}
 
 %\usepackage{enumitem}
 %\setdescription{labelsep=\textwidth}
 
-\author{Benoit Valot\\
-\texttt{valot@moulon.inra.fr}\\
+\author{Benoit Valot and Olivier Langella\\
+\texttt{valot@moulon.inra.fr; langella@moulon.inra.fr}\\
 PAPPSO - \url{http://pappso.inra.fr/}\\
 \includegraphics[width=1cm]{images/pappso.pdf}
 }
 \title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results}
-\date{29 October 2010}
+\date{10 May 2011}
 
 %Modification des entetes et pied de page + marges
 \geometry{top=3cm, bottom=3cm, left=2cm, right=2cm}
@@ -44,12 +44,15 @@ $\X$ is an alternative to the installation of the GPM on local servers.
 $\X$ performs database searching and matching on a list of MS/MS runs in one shot, using a list of easily user selected paramaters and databases.
 
 \paragraph*{}
-$\X$ also performs filtering of data according to statistical values at peptide and protein levels. The results are stored into TSV (Tab Separated Values) files. Moreover, redundancy of protein databases are fully filtered as follows :
+$\X$ also performs filtering of data according to statistical values at peptide and protein levels. Moreover, redundancy of protein databases are fully filtered as follows :
 \begin{itemize}
 \item proteins identified without specific peptides compared to others are eliminated;
 \item proteins identified with the same pool of peptides are assembled;
 \item proteins are grouped by function (identified with at least one common peptide), and the specific peptides for each sub-group of proteins are indicated.
 \end{itemize}
+
+\paragraph*{}
+$\X$ allows to view and edit the filtered results, compute the false discovery rate, ... The results can be exported into TSV (Tab Separated Values) files.
 \end{abstract}
 
 \tableofcontents
@@ -60,7 +63,7 @@ $\X$ also performs filtering of data according to statistical values at peptide
 
 \subsection{License}
 \paragraph*{}
-Copyright (C) 2010  Valot Benoit\\
+Copyright (C) 2010  Valot Benoit and Olivier Langella\\
 $\X$ program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\\
 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the \href{http://www.gnu.org/licenses/gpl.html}{GNU General Public License} for more details.
 
@@ -68,27 +71,21 @@ This program is distributed in the hope that it will be useful, but WITHOUT ANY
 $\X$ works on all platforms (Linux, Windows and Mac). Java 1.6 must be installed (it can be found :
 \href{https://cds.sun.com/is-bin/INTERSHOP.enfinity/WFS/CDS-CDS_Developer-Site/en_US/-/USD/ViewProductDetail-Start?ProductRef=jre-6u14-oth-JPR@CDS-CDS_Developer}{here}).
 
-\subsection{Third party softwares for Windows}
-\begin{enumerate}
-\item Download the \href{http://pappso.inra.fr/downloads/xtandem_pipeline.zip}{$\X$ archive} and unzip it.
-\item Create a folder named "Benperl/" directly in the C:/ directory.
-\item Move the folders "Xtandem", from the archive to the new folder "C:/Benperl/".
-\end{enumerate}
-You could also download the executable in the \href{ftp://ftp.thegpm.org/projects/tandem/binaries/}{GPM site} (32 and 64 bits).
+\subsection{Third party softwares for Windows and Mac}
+Download the X!Tandem executable from the \href{ftp://ftp.thegpm.org/projects/tandem/binaries/}{GPM site}.
 
 \subsection{Third party softwares for Linux}
 \subsubsection*{Ubuntu}
 \begin{itemize}
 \item Add this \href{https://launchpad.net/~olivier-langella/+archive/ppa}{repository}. 
-\item Install the \textit{xtandem-tornado} package.
+\item Install the \textit{xtandem-cyclone} package.
+\item You can also install the \textit{xtandempipeline} package to run \X rather than used jlnp link.
 \end{itemize}
 \subsubsection*{Other distributions}
 \begin{itemize}
 \item Download the \href{ftp://ftp.thegpm.org/projects/tandem/source/}{sources} and follow the instruction of compilation.
 \end{itemize}
 
-\subsection{Third party softwares for Mac}
-Download the executable from the \href{ftp://ftp.thegpm.org/projects/tandem/binaries/}{GPM site}.
 
 \begin{figure}[!ht]
 \center \includegraphics[scale=0.5]{images/tandem_principal.png}
@@ -100,16 +97,17 @@ Download the executable from the \href{ftp://ftp.thegpm.org/projects/tandem/bina
 \paragraph*{}
 To run \X, simply :
 \begin{itemize}
-\item Open X!Tandem pipeline by using this \href{http://pappso.inra.fr/documents/bioinformatique/xtandem_parser.jnlp}{link}
+\item Open X!Tandem pipeline by using this \href{http://pappso.inra.fr/bioinfo/xtandempipeline/xtandempipeline.jnlp}{link}
 \item Wait for the program to execute
 \item The principal window will appear (Fig~\ref{principal})
 \end{itemize}
 
 \subsection{Configuration}
+At the firt start, the application open the configuration path window:
 \begin{itemize}
-\item Open the menu X!Tandem $\rightarrow$ Configuration (Fig~\ref{configuration}).
+\item Open the menu \textit{Option $\rightarrow$ Configuration Path} (Fig~\ref{configuration}).
 \item Define the path to the X!Tandem executable
-\item Choose the folder where to store the X!Tandem parameters
+\item Choose the folder where to store the X!Tandem parameters (or used default one).
 \item Choose the folder where the MS/MS data, the protein databases and the X!tandem results are stored
 \end{itemize}
 
@@ -129,11 +127,11 @@ Three successive graphical boxes help you select first the mzXML files or other
 \subsection{Parameters}
 \label{parameter}
 \paragraph*{}
-To perform database searching, you must create or edit a model XML file (stored in the xtandem models folder). Open the menu X!Tandem $\rightarrow$ Parameters (Fig~\ref{xtandem_parameter}).
+To perform database searching, you must create or edit a model XML file (stored in the xtandem models folder). Open the menu \textit{Option $\rightarrow$ X!Tandem preset} (Fig~\ref{xtandem_parameter}).
 
-\begin{figure}[!h]
+\begin{figure}[!ht]
 \center \includegraphics[scale=0.4]{images/tandem_parameter.png}
-\caption{Parameter window}
+\caption{X!Tandem preset window}
 \label{xtandem_parameter}
 \end{figure}
 
@@ -142,12 +140,12 @@ To use complete performance of your computer, specify the number of CPU in the m
 
 \subsection{Running analysis}
 \paragraph*{}
-To perform analysis, start the menu X!Tandem $\rightarrow$ Analysis.
+To perform analysis, start the menu \textit{File $\rightarrow$ X!Tandem $\rightarrow$ Analysis}. Select on the window (Fig~\ref{xtandem_analysis}) :
 \begin{enumerate}
-\item Select the peak-list files to be analyzed (See~\ref{peak})
-\item Select the database files to be searched (See~\ref{database})
-\item Select the folder where to store the result files
-\item Select the searching parameters model (See~\ref{parameter})
+\item Peak-list files to be analyzed (See~\ref{peak})
+\item Database files to be searched (See~\ref{database})
+\item Searching parameters model (See~\ref{parameter})
+\item Folder where to store the result files
 \end{enumerate}
 
 \subsection{Peak-lists}
@@ -160,6 +158,12 @@ X!Tandem works with open peak-list files like mzXML, mgf, mzData, mzML or pkl fi
 \paragraph*{}
 X!Tandem software uses only protein databases in fasta format. It doesn't work with EST\footnote{Expressed Sequenced tag} sequences. You can transform your database using our application \textit{Protein database manager}, available \href{http://pappso.inra.fr/bioinformatique.html}{here}, or you can directly run it \href{http://pappso.inra.fr/documents/bioinformatique/database_manager.jnlp}{here}.
 
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.4]{images/tandem_analysis.png}
+\caption{X!Tandem parameter window}
+\label{xtandem_analysis}
+\end{figure}
+
 \pagebreak
 
 \section{Processing the results}
@@ -169,7 +173,7 @@ To process results, $\X$ needs to have X!Tandem result files (.xml). The names o
 \subsection{Three modes of analysis}
 \label{mode}
 \paragraph*{}
-You can filter the MS/MS identification results and export them in three different modes : (menu Processing)
+You can filter the MS/MS identification results and export them in three different modes : (menu \textit{File $\rightarrow$ Load Result})
 \begin{description}
 \item[Individual mode] \hfill  \\ Each MS/MS result file is processed individually.\\
 You cannot perform comparison by using this process.
@@ -179,19 +183,13 @@ This mode is useful to compare different results.
 \end{description} 
 
 \paragraph*{}
-In all modes, you have to :
-\begin{enumerate}
-\item Select the XML result files
-\item Define the filter parameters  (~\ref{filtering})
-\item Define the name of the result file to export
-\item Define the export parameters  (~\ref{exporting})
-\end{enumerate}
+In all modes, you have to defined the filter parameters.
 
 \subsection{Filter parameters}
-\label{filtering}
 The filter window (Fig~\ref{filter}) defines the automated filtering process parameters :
 \small
 \begin{description}
+\item[Add files] \hfill \\At this stage, you can add other MS/MS result files to the analysis. If two files have the same name, they are combined in one result file. Interesting if one wants to combine X!Tandem results of the same LC-MS/MS run using different modification parameters or protein databases.
 \item[Peptide E-value] \hfill \\Defines the E-value above which a peptide is considered as valid.
 \item[Peptide number] \hfill \\Defines the number of valid unique\footnote{Unique peptides are defined as peptides with different sequences. This excludes peptides with different modifications.} peptides necessary to validate a protein.
 \item[Protein E-value] \hfill \\Defines the E-value above which a protein is considered as valid.
@@ -202,15 +200,12 @@ The filter window (Fig~\ref{filter}) defines the automated filtering process par
 \item[Sum to all] \hfill \\Defines how protein filter is performed when MS/MS results are combined :
 \begin{description}
 \item[No] To validate a protein, the 2 parameters (peptide number and protein E-value) must be valid in at least one result.
-Interesting if one wants to compare 2DLC-MS/MS results, where peptides from a protein are in the same LC-MS/MS run.
+Interesting if one wants to compare SDS-PAGE-LC-MS/MS results, where peptides from a protein are in the same LC-MS/MS run.
 \item[Yes] To validate a protein, the 2 parameters (peptide number and protein E-value) must be valid in the sum of all results.
-Interesting if one wants to compare SDS-PAGE-LC-MS/MS results, where peptides from a protein are split in different LC-MS/MS runs.
+Interesting if one wants to compare 2DLC-MS/MS results, where peptides from a protein are split in different LC-MS/MS runs.
 \end{description}
-\item[Phosphopeptide] \hfill \\Keep only peptides containing phosphorylated residue modifications.
-All other peptides are invalided.
 \item[Contaminants] \hfill \\When you perform an analysis using different fasta databases, you can remove the result from one database by selecting this database.
 Interesting because it allows you to always include the same contaminant proteins during the database search, and because it removes the contaminant proteins from the results.
-\item[Add results] \hfill \\At this stage, you can add other MS/MS result files to the analysis. If two files have the same name, they are combined in one result file. Interesting if one wants to combine X!Tandem results of the same LC-MS/MS run using different modification parameters or protein databases.
 \end{description}
 \normalsize
 \begin{figure}[!ht]
@@ -221,6 +216,73 @@ Interesting because it allows you to always include the same contaminant protein
 
 \pagebreak 
 
+
+\section{View and edit the results}
+\label{viewing}
+
+After loading the results, you can select the result to view in the principal window (Fig~\ref{principal}). After this selection, you can navigate in this result in four different windows listed in the menu \textit{Windows} :
+
+\subsection{Proteins List}
+View the list of protein identified on the result. For more details on column see Fig~\ref{prot}.
+\begin{itemize}
+\item Filter the protein by description;
+\item Clic on a protein to view the corresponding peptides list (see ~\ref{peptide_list}) and protein details (see ~\ref{protein_details});
+\item Unchecked protein for unvalidate the corresponding peptides;
+\item \textbf{Applied modification} to validate the edition.
+\end{itemize}
+
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/window_protein.png}
+\caption{Proteins List}
+\end{figure}
+
+\subsection{Protein Details}
+\label{protein_details}
+View the protein sequence and coverage on a identified protein. To view this window, you must open it in the menu \textit{Windows $\rightarrow$ Protein details}.
+
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.7]{images/window_protein_detail.png}
+\caption{Protein details}
+\end{figure}
+
+\subsection{Peptides List}
+\label{peptide_list}
+View the peptides identified a protein. For more details on column see Fig~\ref{pep}. 
+
+\begin{itemize}
+\item Filter the peptide by different options;
+\item Clic on a peptide to view the corresponding MS/MS spectra (see ~\ref{peptide_detail});
+\item Unchecked peptide for unvalidate it.
+\end{itemize}
+
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/window_peptide.png}
+\caption{Peptides List}
+\end{figure}
+
+\subsection{Peptides Details}
+\label{peptide_detail}
+View the MS/MS spectra of an identified peptide.
+
+\begin{itemize}
+\item Clic on spectra to zoom.
+\item Save MS/MS annotated spectra on png or svg.
+\end{itemize}
+
+\begin{figure}[!ht]
+\center \includegraphics[scale=0.5]{images/window_peptide_detail.png}
+\caption{Peptides Details}
+\end{figure}
+
+\section{Save and Load X!Tandem Pipeline project}
+\paragraph{}
+You can save all the current results using menu \textit{File $\rightarrow$ Save Project}, or load an previous one using menu \textit{File $\rightarrow$ Load Project}. The extension of created files is \textit{*.xpip}.
+
+\pagebreak
+
+\section{Exporting the results}
+You can export the result in different formats in menu \textit{File $\rightarrow$ Export}.
+
 \subsection{Export parameters}
 \label{exporting}
 The export window (Fig~\ref{export}) shows the different types of available exports :
@@ -229,8 +291,7 @@ The export window (Fig~\ref{export}) shows the different types of available expo
 \item[Default] \hfill \\Creates TSV files containing identification results for proteins (*protein.txt) and peptides (*peptide.txt). When you perform a combined analysis, a *compar.txt file is created that contains the results of comparison between samples.
 \item[Fasta] \hfill \\Creates a fasta file for valid proteins.
 \item[PepNovo] \hfill \\Creates a XML file containing the peptide results to be removed for an automated \textit{De Novo} interpretation in sequence using our \href{http://pappso.inra.fr/documents/bioinformatique/DeNovo_pipeline.pdf}{DeNovo pipeline}.
-\item[FDR] \hfill \\Creates a tabulated file containing the number of valid peptides for the different peptide E-values in each database. Allows you to determine the E-value above which FDR value is acceptable.\\
-\label{fdr}\textbf{Warning} : Use very low parameters in peptide (0.1) and protein (-1) E-values, and set the number of unique peptides to validate a protein to 1.
+\item[FDR] \hfill \\Creates two tabulated files containing the number of valid peptides or valid proteins for the different E-values in each database. Allows you to determine the E-value above which FDR value is acceptable.
 \item[Protic] \hfill \\Creates a PROTICdb compatible XML file, so you can store results in the \href{http://pappso.inra.fr/bioinformatique.html}{PROTICdb} proteomic database.
 \item[MassChroQ] \hfill \\Creates a MassChroQ compatible XML file, so you can perform quantitative analysis using our home-made software \textbf{MassChroQ} (to be released soon).
 \end{description}
@@ -241,9 +302,6 @@ The export window (Fig~\ref{export}) shows the different types of available expo
 \label{export}
 \end{figure}
 
-\pagebreak
-
-\section{Exporting the results}
 \subsection{Files *protein.txt}
 The identified proteins are represented by sample (individual mode) or for all samples (combine/phosphopeptide modes) (Fig~\ref{prot}). Proteins are grouped by function.
 \small
@@ -348,17 +406,18 @@ The list of proteins is repeated 4 times, corresponding to the 4 parameters that
 
 \subsection{Files *fdr.txt}
 This result file indicates the number of peptides with an E-value less than the E-value indicated in the fist column (Fig~\ref{fdr2}). You just have to divide the number of peptides in the reverse or decoy database by the number of peptides in the normal database to obtain the false discovery rate at each E-value level.\\
-This method has 2 limitations :
+This method could be performed if :
 \begin{itemize}
 \item normal and reverse databases must be saved in different fasta files;
-\item the filter parameters must be low (~\ref{fdr})
+\item X!tandem analysis have been performed with reverse option.\\ 
+In this case, the column corresponding to the normal and reverse search are indicated as \textit{xtandem normal} and \textit{xtandem reverse}, respectively.
 \end{itemize}
 
-\begin{figure}[!h]
+\begin{figure}[!ht]
 \center \includegraphics[scale=0.5]{images/tandem_fdr.png}
 \caption{FDR results}
 \label{fdr2}
 \end{figure}
 
 
-\end{document}
\ No newline at end of file
+\end{document}

xtandempipeline/share/xtandempipeline/xtandempipeline.jnlp

@@ -16,7 +16,7 @@
     <all-permissions />
   </security>
   <resources>
-    <j2se version="1.6+" java-vm-args="-ea -Xincgc -verbose -Xmx1600m -Xms256m" />
+    <j2se version="1.6+" java-vm-args="-ea -Xincgc -Xmx1000m -Xms256m" />
     <jar href="XtandemPipeline.jar" main="true" download="eager" />
         
     <!--	  	    
@@ -62,26 +62,34 @@
     <jar href="lib/swt/swt-win32-windows-x86.jar" />
   </resources>
   <resources os="Windows" arch="x86_64">
-    <j2se version="1.6+" />
+    <j2se version="1.6+" java-vm-args="-ea -Xincgc -Xmx1500m -Xms256m" />
     <jar href="lib/swt/swt-win32-windows-x86_64.jar" />
   </resources>
   <resources os="Linux" arch="x86_64">
-    <j2se version="1.6+" />
+    <j2se version="1.6+" java-vm-args="-ea -Xincgc -Xmx1900m -Xms256m" />
     <jar href="lib/swt/swt-gtk-linux-x86_64.jar" />
   </resources>
   <resources os="Linux" arch="amd64">
-    <j2se version="1.6+" />
+    <j2se version="1.6+" java-vm-args="-ea -Xincgc -Xmx1900m -Xms256m" />
     <jar href="lib/swt/swt-gtk-linux-x86_64.jar" />
   </resources>
   <resources os="Linux" arch="x86">
-    <j2se version="1.6+" />
+    <j2se version="1.6+" java-vm-args="-ea -Xincgc -Xmx1400m -Xms256m" />
     <jar href="lib/swt/swt-gtk-linux-x86.jar" />
   </resources>
   <resources os="Linux">
-    <j2se version="1.6+" />
+    <j2se version="1.6+" java-vm-args="-ea -Xincgc -Xmx1400m -Xms256m" />
     <jar href="lib/swt/swt-gtk-linux-x86.jar" />
   </resources>
-  
+  <resources os="Mac\ OS\ X" arch="i386">
+  <j2se version="1.6+" java-vm-args="-ea -Xincgc -XstartOnFirstThread -Xmx1000m -Xms256m"/>
+  <jar href="./swt/swt-cocoa-macosx-x86-3.6.1.jar" />
+  </resources>
+  <resources os="Mac\ OS\ X" arch="x86_64">
+  <j2se version="1.6+" java-vm-args="-ea -Xincgc -XstartOnFirstThread -Xmx1900m -Xms256m"/>
+  <jar href="./swt/swt-cocoa-macosx-x86_64-3.6.1.jar" />
+  </resources>
+
 	<application-desc main-class="fr.inra.pappso.xtandempipeline.XtandemPipelineMain" >
 	</application-desc>