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Tutorial for Novice Users

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dahoehn edited this page Jan 31, 2025 · 3 revisions

This page aims to explain how to run qAlgorithms from the terminal to those with no experience with command line tools.

Before you can begin processing, make sure to download all four required files linked in the readme.

The directory in which you set up qAlgorithms should look like this:

folder_setup

Next, locate the files which you want to process. As an example, we will process one file by specifying the directory in which it is saved. qAlgorithms can only process .mzML files, not .mzXML, at the moment.

data_dir

To run qAlgorithms, you have to start it from powershell. Double-clicking the .exe will not do anything. You can start powershell by entering "powershell" into the field where the location of your current folder is shown:

powershell_text

Press "enter" to run powershell in the qAlgorithms directory. powershell_open

Note that in powershell, you can not move the cursor with the mouse like in a text editor, so use the arrow keys.

You can now start qAlgorithms. To make sure the program works, first enter the command ./qAlgorithms.exe -h and press "enter" to execute it:

help_output

If the help menu appears, qAlgorithms will (probably) work on your system.

We can now process the file mentioned above. To this end, run qAlgorithms with input location, output location and output type specified.

  • The input location is specified with the -i argument. Enter the path to the file or the directory of files you want to process.
  • The output location is a directory specified with the -o argument. Your results will be saved to this location as .csv files.
  • The output type allows you to print intermediate results into separate files. To print the feature list, use '-pf'. For further options, refer to the manual page printed with ./qAlgorithms -help.

You can click and drag the input and output locations instead of typing them out. Execute the command by pressing "enter":

process_command

If the program runs successfully, a log message will be printed to the terminal. The output path is also included in the log message. In this case, it is the same directory in which we have our input file saved:

output_dir

You can also use the * character as a wildcard when selecting the input path. Assuming you have a directory which contains samples, blanks and standard mixtures, but you only want to process the standards for now, you can write:

./qAlgorithms.exe -i ./your_data/*_std* -o . -pf

Wildcards obviously only work for selecting the input files, since multiple output locations are not supported by qAlgorithms.

Contents of the qAlgorithms wiki are licensed under CC BY-NC 4.0.

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