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Question: Named Command Line Argument Conventions
0
gravatar for Bob
2.1 years ago by
Bob • 0
United States
Bob • 0 wrote:

Are there any Galaxy community standards for identifying command line arguments by name?

We are adapting a suite of tools to work in Galaxy and we're writing the "glue" code that will pass parameters from the Galaxy GUI to our tools. All of the examples I've seen so far show positional parameters passed on the command line. We would like to use named parameters something like this:

tool a=5 b=8
tool -a 5 -b 8

We can write our code to meet any standard, and I was wondering if there are any conventions that we might want to follow. Any thoughts?

Thanks in advance.
tool development galaxy wrapper • 666 views
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modified 2.1 years ago • written 2.1 years ago by Bob • 0
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gravatar for Devon Ryan
2.1 years ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

Have a look at the deepTools wrappers, which use a lot of optional switches both with and without arguments.
ADD COMMENT • link written 2.1 years ago by Devon Ryan • 1.9k
0
gravatar for Bob
2.1 years ago by
Bob • 0
United States
Bob • 0 wrote:

Thanks for the tip. I looked at some of the documentation and they appear to be using the common Linux/UNIX/GNU syntax:

bamCoverage --bam a.bam -o a.SeqDepthNorm.bw --binSize 10 --normalizeTo1x 2150570000 --ignoreForNormalization chrX --extendReads

deepTools2.0/bin/bamPEFragmentSize -hist fragmentSize.png -T "Fragment size of PE RNA-seq data" --maxFragmentLength 1000 -b testFiles/RNAseq_sample1.bam

That's fortunate since we're writing in Python and the argparse module handles that format naturally.

Thanks for the response.
ADD COMMENT • link modified 2.1 years ago • written 2.1 years ago by Bob • 0
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