Mercurial > repos > pieterlukasse > prims_proteomics
changeset 23:03e49edb0e90 default tip
Merge heads at 12:8db345e67278 and 22:fa1eef8595dc which were created as a result of a recently fixed bug.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Mon, 13 Jan 2014 12:38:18 -0500 |
| parents | fa1eef8595dc (diff) 8db345e67278 (current diff) |
| children | |
| files | README.rst |
| diffstat | 18 files changed, 58 insertions(+), 233 deletions(-) [+] |
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--- a/README.rst Mon Dec 30 14:21:23 2013 +0100 +++ b/README.rst Mon Jan 13 12:38:18 2014 -0500 @@ -1,11 +1,13 @@ -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 +Proteomics module of Plant Research International's Mass Spectrometry (PRIMS) toolsuite. +This toolset consists 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). +with PRIMV-visualization (primv_visualization package). + Copyright 2010-2013 by Pieter Lukasse, Plant Research International (PRI), Wageningen, The Netherlands. All rights reserved. See the license text below. @@ -15,228 +17,51 @@ 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 +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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--- a/csv2apml.xml Mon Dec 30 14:21:23 2013 +0100 +++ b/csv2apml.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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: @@ -119,7 +119,7 @@ ----- -**Output ** +**Output** This tools returns the input data in APML xml format.
--- a/msfilt.xml Mon Dec 30 14:21:23 2013 +0100 +++ b/msfilt.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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: @@ -37,8 +37,8 @@ SEDMAT or Quantiline tools." /> <repeat name="annotationSourceFiles" title="(Optional) Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> - <param name="identificationsFile" type="data" format="apml,mzidentml,mscfileset" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> - <param name="spectraFile" type="data" format="mzidentml,mscfileset" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)" + <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> + <param name="spectraFile" type="data" format="mzidentml,prims.fileset.zip" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)" help="Select this in case your Identifications file is MZIDENTML or MZIDENTML fileSet" /> </repeat>
--- a/napq.xml Mon Dec 30 14:21:23 2013 +0100 +++ b/napq.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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 @@ -21,8 +21,8 @@ <inputs> <repeat name="identificationFileList" title="Peptide identification files" help="Full set of MS/MS peptide identification files, including peptides that could not be quantified."> - <param name="identificationsFile" type="data" format="apml,mzidentml,mscfileset" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> - <param name="spectraFile" type="data" format="mzidentml,mscfileset" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)" + <param name="identificationsFile" type="data" format="apml,mzidentml,prims.fileset.zip" label="Identifications file (APML or MZIDENTML or MZIDENTML fileSet)" /> + <param name="spectraFile" type="data" format="mzidentml,prims.fileset.zip" optional="true" label="(Optional) Spectra fileSet (mzml file or fileSet)" help="Select this in case your Identifications file is MZIDENTML or MZIDENTML fileSet" /> </repeat>
--- a/prims_proteomics_datatypes.py Mon Dec 30 14:21:23 2013 +0100 +++ b/prims_proteomics_datatypes.py Mon Jan 13 12:38:18 2014 -0500 @@ -37,6 +37,6 @@ class Apml( ProteomicsXml ): """APML data""" - file_ext = "pepxml" + file_ext = "apml" blurb = 'PRIMS APML proteomics data' root = "apml" \ No newline at end of file
--- a/progenesisconverter.xml Mon Dec 30 14:21:23 2013 +0100 +++ b/progenesisconverter.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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 14:21:23 2013 +0100 +++ b/quantifere.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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 14:21:23 2013 +0100 +++ b/quantiline.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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: @@ -17,8 +17,8 @@ </command> <inputs> - <param name="ppidsFileName" type="data" format="mscfileset" label="MS/MS peptide identifications fileSet (N mzidentml files)"/> - <param name="spectraDataFile" type="data" format="mscfileset" label="MS/MS spectra fileSet (N mzml files)"/> + <param name="ppidsFileName" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/> + <param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/> <param name="labelMzValues" type="text" size="20" label="Label m/z values" help="e.g. for 4plexed iTRAQ : 114.0,115.0,116.0,117.0"/>
--- a/repository_dependencies.xml Mon Dec 30 14:21:23 2013 +0100 +++ b/repository_dependencies.xml Mon Jan 13 12:38:18 2014 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories description="Required proteomics dependencies."> <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="09b89b345de2" /> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="7101f7e4b00b" /> </repositories>
--- a/sedmat.xml Mon Dec 30 14:21:23 2013 +0100 +++ b/sedmat.xml Mon Jan 13 12:38:18 2014 -0500 @@ -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: @@ -73,8 +73,8 @@ <option value="mzid" selected="true">mzIdentML on mzML</option> </param> <when value="mzid"> - <param name="spectraDataFile" type="data" format="mscfileset" label="MS/MS spectra fileSet (N mzml files)"/> - <param name="ppidsFile" type="data" format="mscfileset" label="MS/MS peptide identifications fileSet (N mzidentml files)"/> + <param name="spectraDataFile" type="data" format="prims.fileset.zip" label="MS/MS spectra fileSet (N mzml files)"/> + <param name="ppidsFile" type="data" format="prims.fileset.zip" label="MS/MS peptide identifications fileSet (N mzidentml files)"/> </when> </conditional> </when>