diff README.md @ 1:8bac3cc5c5de draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847

--- a/README.md	Fri May 10 17:22:51 2013 -0400
+++ b/README.md	Sat Jul 20 05:01:05 2019 -0400
@@ -1,34 +1,27 @@
-Tool wrapper for MaxQuant. 
+GalaxyP - MaxQuant
+==================
 
-MaxQuant is a Windows only program and so you will likely need to
-deploy this tool to run on a remote Windows system via the LWR
-(https://lwr.readthedocs.org).
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
+* Tool ID: `maxquant`
+* Tool Type: `default`
 
-The sample mods file maxquant_mods.loc.sample corresponds to the
-default modifications MaxQuant is configured with. The Galaxy-P
-project uses a MaxQuant that has been extended with all of Unimod. To
-modify MaxQuant in this fashion replace MaxQuant's modifications.xml
-file with the extended_modifications.xml distributed with this tool
-and configure Galaxy with the maxquant_mods.loc.sample.extended loc
-file.# Obtaining Tools
 
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
+Description
+-----------
+
+Wrapper for the MaxQuant version available in conda.
+
 
-# Contact
-
-Please send suggestions for improvements and bug reports to
[e-mail].
-
-# License
+Updating
+--------
 
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
-
-# Tool Versioning
+MaxQuant often changes the layout of its parameters file.
+So changes to the code are likely to be necessary when
+updating to a new version of MaxQuant. The init.py script
+can be used to initialize the tool with a new list of
+modifications or enzymes. From the tool dir run:
 
-Galaxy-P tools will have versions of the form X.Y.Z. Versions
-differing only after the second decimal should be completely
-compatible with each other. Breaking changes should result in an
-increment of the number before and/or after the first decimal. All
-tools of version less than 1.0.0 should be considered beta.
+./init.py -m MODIFICATIONS.XML -e ENZYMES.XML
+
+The location of these xml files usually is:
+ANACONDA_DIR/bin/conf/
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