diff README.rst @ 48:b72821cab1d7 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"

--- a/README.rst	Thu Feb 20 10:51:14 2020 +0000
+++ b/README.rst	Fri Jan 15 14:05:46 2021 +0000
@@ -3,7 +3,7 @@
 
 - Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
 - Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker>
-- Tool ID: `peptideshaker`, `search_gui`
+- Tools ID: `peptide_shaker`, `search_gui`, `ident_params`, `fasta_cli`
 
 
 Description
@@ -11,13 +11,23 @@
 
 Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker.
 
-Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these.  It creates a large zip archive with all search results, the original database and spectra.  This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
+Includes tool wrappers for FastaCLI, IdentificationParametersCLI, SearchGUI and PeptideShaker.
+
+
+
+FastaCLI adds decoy sequences to any fasta file.
+
+The Identification Parameters tool allows to create a parameters (par) file which can be (re)used later to parameterize SearchGUI or PeptideShaker.
+
+The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra.
+
+This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
 
 
 General Requirements
 --------------------
 
-This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
+To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
 
     export _JAVA_OPTIONS='-Xmx1500M'
 
@@ -31,34 +41,23 @@
 -----------------
 
 Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required.  If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually.
-  
+
 On ubuntu Mono can be installed as follows
 
 	sudo apt-get install mono-runtime
 	sudo apt-get install libmono-system-core4.0-cil
 
-For more help on installing Mono please see http://www.mono-project.com/download. 
+For more help on installing Mono please see http://www.mono-project.com/download.
 
 Note
 ----
 
-- Requires Galaxy release v15.10 or later, which fixes the installation of package_peptideshaker_1_1 and provides a searchgui_archive datatype that includes a version
-
-- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.
+- Requires Galaxy release v16.01 or later.
 
 See:
 
-* <https://code.google.com/p/peptide-shaker/>
-* <https://code.google.com/p/searchgui/>
-
-
-Search GUI - Fixed and Variable Modifications
--------------------------------------------
-
- - Options for modifications are read from local data file: searchgui_mods.loc
-   This is copied from searchgui_mods.loc.sample on the first installation.  
-
-The modifications are from:  https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/identification/search_parameters_cli/IdentificationParametersInputBean.java
+* <http://compomics.github.io/projects/peptide-shaker.html/>
+* <http://compomics.github.io/projects/searchgui.html/>
 
 GalaxyP Community
 -----------------
@@ -101,3 +100,4 @@
 * Gerben Menschaert
 * Elvis Ndah
 * Minnesota Supercomputing Institute, Univeristy of Minnesota
+* Carlos Horro