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README.md
 
 
deep_process_schema.xsd
 
 
deep_process_style.css
 
 
deep_process_template.xml
 
 
Templates for new documents Create a new Process document Technical note: encoding Technical note: style sheet Validate the new Process document

README.md

Templates for new documents

Create a new Process document

In order to document a new analysis, please download the file deep_process_template.xml and fill out all sections with your favorite text or XML editor. Certain entries must appear only once (Process name, version and author as well as the description), whereas the remaining sections can contain as many entries as needed; you can list any number of input, output and reference files and as many tools as needed in the Software section to give a complete step-by-step documentation of the analysis pipeline.

An important note: please verify that the template you are using lists the following style sheet document at the top:

<?xml version="1.0"?>
<?xml-stylesheet type="text/css" href="http://deep.mpi-inf.mpg.de/DAC/files/style/deep_process_style.css"?>

This is required to render the Process XML file into a nicely readable form when opened with a standard web browser. Also, please make sure that there is no encoding specified, i.e., the following is considered bad practice:

<?xml version="1.0" encoding="ISO-8859-1"?>
<?xml-stylesheet type="text/css" href="http://deep.mpi-inf.mpg.de/DAC/files/style/deep_process_style.css"?>

For a more detailed description, please refer to the following publication:

"A general concept for consistent documentation of computational analyses", Database 2015

Technical note: encoding

If you are wondering why there should no encoding be specified in the Process document itself: the encoding for all DEEP Process files is set in the XML schema file. This ensures that all Process files are read with the same encoding when using the validation script and the respective schema file.

Technical note: style sheet

If you are wondering why the link the Process template does not refer to this repository: repositories are not meant for file hosting like a regular web server. To discourage users from nevertheless doing so, the Github software forces the MIME type of the style sheet document to be text/plain instead of text/css when it is loaded in your browser. Unfortunately, the browser cannot recognize (interpret) the style sheet as such in this scenario and, hence, the Process document would not be rendered as intended.

Validate the new Process document

After having created a new Process document, the most convenient way to check it for syntactical errors (e.g., missing software versions or invalid characters) is to use the small Python script provided in this repository validation script.