I am stuck on how to implement filtering on the command line using the galaxy tools. Specifically, I want to do this for the command line. I want to use the following filtering parameters:
- Input parameter: value
- Minimum size: 40
- Maximum size: 0
- Minimum Quality: 30
- Maximum Quality: 0
- Maximum number of bases allowed outside of quality range: 5
- Obtain fastq_filter from devteam toolshed found here
- Took a look at the sourcode fastq_filter.py, this is where I got stuck. Please see below:
#Read command line arguments
input_filename = sys.argv
script_filename = sys.argv
output_filename = sys.argv
additional_files_path = sys.argv
input_type = sys.argv or 'sanger'
What the heck is the script_filename and additional_files_path? I see no where in the input for the values that the usegalaxy.org asks for? I would appreciate any assistance that would be rendered.