Mercurial > repos > pieterlukasse > prims_proteomics
changeset 14:a84eb3eb8749
changed versions and README file
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Mon, 30 Dec 2013 14:46:34 +0100 |
| parents | ce5d7b020748 |
| children | 2479eff53fc8 |
| files | README.rst csv2apml.xml msfilt.xml napq.xml progenesisconverter.xml quantifere.xml quantiline.xml sedmat.xml |
| diffstat | 8 files changed, 34 insertions(+), 210 deletions(-) [+] |
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--- a/README.rst Mon Dec 30 08:27:11 2013 -0500 +++ b/README.rst Mon Dec 30 14:46:34 2013 +0100 @@ -1,11 +1,12 @@ -PRIMS-proteomics toolset and Galaxy wrappers -============================================ +PRIMS-proteomics toolset & Galaxy wrappers +========================================== Tools and wrappers for the PRIMS-proteomics toolset. Suite of custom tools to enable data processing and protein inference for labeled and label-free Mass Spectrometry proteomics data. Can be used in combination with PRIMS-MASSCOMB (prims_masscomb package) and with PRIMV-visualizations (primv_visualizations package). + Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), Wageningen, The Netherlands. All rights reserved. See the license text below. @@ -15,221 +16,44 @@ History ======= -======= ====================================================================== -Version Changes -------- ---------------------------------------------------------------------- -v1.0.2 - Final version as part of the Galaxy main repository, and the - first release via the Tool Shed -v1.0.1 - Version used internally at PRI before release via Toolshed +============== ====================================================================== +Date Changes +-------------- ---------------------------------------------------------------------- +January 2014 -first release via Tool Shed +November 2013 -multiple tools used internally at PRI +end 2011 -first tool +============== ====================================================================== + +Tool Versioning +=============== + +PRIMS 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. -Bug Reports and other questions -=============================== +Bug Reports & other questions +============================= For the time being issues can be reported via the contact form at http://www.wageningenur.nl/en/Persons/PNJ-Pieter-Lukasse.htm -Developers, Contributions and Collaborations +Developers, Contributions & Collaborations ========================================== If you wish to join forces and collaborate on some of the tools do not hesitate to contact Pieter Lukasse via the contact form above. + License (Apache, Version 2.0) ============================= - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] + Copyright 2013 Pieter Lukasse, Plant Research International (PRI). Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. + you may not use this software except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0
--- a/csv2apml.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/csv2apml.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,4 +1,4 @@ -<tool name="Csv2Apml" id="csv2apml" version="1.0.1"> +<tool name="Csv2Apml" id="csv2apml" version="1.0.2"> <description>Converts MS/MS data in CSV format to APML format</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter:
--- a/msfilt.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/msfilt.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,4 +1,4 @@ -<tool name="MsFilt" id="msfilt" version="1.0.1"> +<tool name="MsFilt" id="msfilt" version="1.0.2"> <description>Filters annotations based MS/MS peptide identification and annotation quality measures</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter:
--- a/napq.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/napq.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,5 +1,5 @@ -<tool name="NapQ" id="napq" version="1.0.2"> - <description>[[experimental]]'no alignment'(alignment-free) peptide quantification</description> +<tool name="NapQ" id="napq" version="0.0.1"> + <description>'no alignment'(alignment-free) peptide quantification</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
--- a/progenesisconverter.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/progenesisconverter.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,4 +1,4 @@ -<tool name="ProgenesisConverter" id="progenesisconv1" version="1.0.1"> +<tool name="ProgenesisConverter" id="progenesisconv1" version="1.0.2"> <description>Converts Progenesis aligned feature lists in CSV format to APML</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter:
--- a/quantifere.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/quantifere.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,4 +1,4 @@ -<tool name="Quantifere" id="quantifere1" version="1.0.1"> +<tool name="Quantifere" id="quantifere1" version="1.0.2"> <description>Protein Inference by Peptide Quantification patterns</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: @@ -6,7 +6,7 @@ ////////////////////////// --> <command interpreter="java -jar "> - Quantifere.jar + Quantifere.jar -annotatedQuantificationFilesList $annotatedQuantificationFilesList -identificationFilesList $identificationFilesList -statisticalMeasuresConfigFile $statisticalMeasuresConfigFile
--- a/quantiline.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/quantiline.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,4 +1,4 @@ -<tool name="Quantiline" id="quantiline1" version="1.0.1"> +<tool name="Quantiline" id="quantiline1" version="1.0.2"> <description>Labeled ms/ms data pre-processing for Protein Quantification (and Inference) pipelines</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter:
--- a/sedmat.xml Mon Dec 30 08:27:11 2013 -0500 +++ b/sedmat.xml Mon Dec 30 14:46:34 2013 +0100 @@ -1,4 +1,4 @@ -<tool name="SedMat" id="sedmat1" version="1.0.1"> +<tool name="SedMat" id="sedmat1" version="1.0.2"> <description>Matches MS and MS/MS results</description> <!-- For remote debugging start you listener on port 8000 and use the following as command interpreter: