xml-parser-nico

A simple project to get dataframe of signal countings from CellCounter_Marker_File XML file

Quickstart

Make sure you have RScript installed on your computer. To verify it, run the following command:

Rscript --version

Help menu of CLI app is called by appending -h|--help flag:

To use the app you must provide a name or absolute path to one of the following:

• .xml file with valid structure of CellCounter_Marker_File (not check yet, program will just crash)
• .txt or .list file with each line containing a name or absolute path to the .xml file.

Recursive search is allowed, meaning your .txt or .list file may contain other .txt or .list files, just make sure to include .xml files somewhere.

NOTE: extensions are mandatory for now, in one of the future updates I will try to check for those as well.

If the program cannot find valid XML on the path it will make a short pause to give you opportunity to halt the program and fix typos. This is done, because when launched in terminal, programs written in R don't wait for a response to the input, which makes input validation quite difficult. Same will happen when you try to overwrite existing .RData file.

Flags

-i/--input - allows to append the data obtained in current parsing to existing .RData file. Just make sure that the countings have the same structure -o/--output - allows to specify name of resulting RData file. When writing both input and output files, extension is mandatory! If -o is missing, filename defaults to timestamp+dp (thinking about including the Image_Filename from initial XML).

Final words

Please write issues on Github if there are problems, this is my first real-life project, and I'm looking forward to making it more advanced!