The aim of this project is to provide a standalone application for microarray layout data file conversion from ADF format to MAGE-ML file format or contrary.
The application has two functionalities:
The tool is a standalone Java application using the MAGE Software Toolkit (MAGE-stk) from the MGED Open source project.
Early specifications can be found there.
A description of the XMLSchema used for XML describing ADF file structure
ADF MAGE-ML Tool Wiki Page (can be used as How To, especially for troubleshooting)
A list of used API and version number is available on this page.
ADF MAGE-ML Tool Mailing List (Subscribe)
MAGE.
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Provided below is a stand-alone application in java for the conversion from ADF format to MAGE-ML file format and vice versa.
(You are welcome to use this documentation and scripts on this page, however, we do not take any responsibilities for their use. Please read our license for more details.)
The tool is developped for Java 1.4 or later. It may work with an earlier version (1.3), but not tested. It has been tested with the Sun Java Virtual Machine, under GNU/Linux Debian and Microsoft Windows 1.5. Tests with free JVM will be done for upcoming version.
The tool has been developed to be used on a desktop computer. However, it required a large quantity of memory. For large data file, it recommands to have at least 1 Gb of memory and 1.5 GHz CPU.
cvs -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/adfconverter login cvs -z3 -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/adfconverter co -P adfconverter-devA development cvs snapshot is available.
Or compiled as archive files : tar.gz, tar.bz2, zip. The source code is also available in archive files, with distribution files.
Last version: 1.0
Changes: reported changes
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The installer (created with IzPack) installs automatically the Tool containing four packages: Base (Mandatory), Documentation, Source, Examples
To install with the installer:
java -jar ADF_MAGEML_Tool-VERSION.jar
Then, follow instructions.
The installer creates automatically the configuration file and the script to launch the tool.
There are two kinds of installer:
Instructions
unzip ADF_MAGEML_Tool-VERSION.zip
tar xzvf ADF_MAGEML_Tool-VERSION.tgz
tar xjvf ADF_MAGEML_Tool-VERSION.tar.bz2
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A script is called to launch the tool. The script sets the ADFCONVERTERHOME variable and calls the tool.
adfconverter.bat
adfconverter.sh
Prior to call the script, please the ADFCONVERTERHOME variable to the path of the directory containing tool files.
Thanks to the ADFCONVERTERHOME variable, the script can be called from anywhere.
ADF MAGE-ML Tool - EBI Tue, 23 Aug 2005 European Bioinformatics Institute - MicroArray Informatics Team Home Page: http://adfconverter.sourceforge.net/ Developed by: Pierre MARGUERITE Version 1.0 ADF MAGE-ML Tool [options] file parameters: file : file or directory to convert Options -t || -text : for text format output -xls : for xls format output -c || -conf : for specific configuration file -check : For checking mode -conv : For conversion mode -strict : strict data checking mode -relax : relax data checking mode (default) -stepbystep : step by step checking mode -nostepbystep : no step by step checking mode (default) -dtd pathtoMAGE-MLDTD: path to the MAGE-ML dtd path -sort: sorting ADF in the given directory -curation: curation of ADFs and save into file -adf: The application only treats ADF files -mage: The application only treats MAGE-ML files -accnumberchecking: The database accession numbers will be checked against the database tag -ontologychecking: The MGED ontology term will be checked -noaccnumberchecking: The database accession numbers will not be chec ked against the database tag -noontologychecking: The MGED ontology terms will be checked -I: Info logging level -D: Debug logging level -update resourcename: update the resourcename (Internet connection re quired) -updateall: update all available resources. (Internet connection re quired) -resources: list of available resources for update.
For treating an ADF file, the path to the ADH file or simply the path without file extension is given as parameter.
ADF file must be in the new ADF format composed of three parts/files.
Start a checking, conversion
adfconverter.bat -I examples/ADF-conversion-test1-correct.adh
Update a resource.
adfconverter.bat -update approveddb
A script is called to launch the tool. The script sets the ADFCONVERTERHOME variable and calls the tool.
adfSimpleGUI.bat
adfSimpleGUI.sh
Prior to call the script, please set the ADFCONVERTERHOME variable to the path of the directory containing tool files.
Thanks to the ADFCONVERTERHOME variable, the script can be called from anywhere.
ADF MAGE-ML Tool - EBI Tue, 23 Aug 2005 European Bioinformatics Institute - MicroArray Informatics Team Home Page: http://adfconverter.sourceforge.net/ Developed by: Pierre MARGUERITE Version 1.0 ADF MAGE-ML Tool [options] file parameters: file : file or directory to convert Options -h || --helptext : for this help -lf || --lookandfeel look and feel name : for setting the UI look and feel --availablelookandfeel lookAndFeelname : Retrieve list of availab le UI look and feels -l || --lang : for setting the UI locale/language
Simply start the GUI
adfSimpleGUI.sh
Set UI language
adfSimple.sh -l fr
Once GUI launch, select a file and check needed options, then click on the "launch" button. You can have additional information on the tool by clicking on the "About" button. From the about window, you can modify tool configuration/default options and update resources.
For ADF, the file given in parameter can be:
The three ADF text file have to have the adh, adr ,adc extension. After treatment, there are one log file per ADF file (adh,adr,adc if present) and a global one (ADF name with .log extension).
For MAGE-ML file, the allowed file extension is ".xml" (case insensitive).
Path to archive file can be provided to the application. Files are uncompressed by the application in a directory called by the name of the archive file. Uncompressed files are erased at the end of treatment. Once uncompressed, the whole newly created directory is treated by the tool.
Supported file extension are:
The ".tar.gz" support is not fully functional. (should be available fix in the next release)
Several information are provided to the tool.
There is currently two type of log:
The log is powered bu the Log4J API.
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Please contact Pierre Marguerite or send a message to the General Mailing List -adfconverter-general@lists.sourceforge.net- (Archive, Subscribe) for more information or use of the ADF MAGE-ML Tool.
Feedbacks are welcome for upcoming version of the tool. Please use needed trackers:
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You are welcome to use this documentation and scripts on this page, however, we do not take any responsibilities for their use.
Please read our license (OSI approved).
ADF MAGE-ML Tool is written in (and requires) Java, and should work on any platform that support Java 1.4.1 or later. Note however, that the tool have currently been compiled and tested on Microsoft Windows, and GNU/Linux (Debian Unstable). It should work on other platforms, but we have no way of testing this ourselves.
Last modified: Mon Oct 24 15:35:51 GMT Daylight Time 2005