Create Galaxy/Pise wrapper from XML or StdOut (myprog --help), or just display options from a galaxy workflow...

Main goal is to provide a simple tool to create simple skeleton XML wrappers file for Galaxy or even Pise (a very old framework from Pasteur institute (now replaced by Mobyle ) )

• Yes, but how ?

That is quite easy:

git clone https://github.com/remyd1/XMLparser-wrapper.git
cd XMLparser-wrapper
python ParserConverterXML.py --help
python ParserConverterXML.py h2gw -c "ls --help" -o ../ls.gw.xml

• Now, it is full of questions... ?!

Relax, it is just to help the program to parse the output. Otherwise, answer "A", to have an automatic parsing process. However, if you want to get all options exactly, you will have to parse it manually with the program.

Answer 'S' for short options (those with just a single dash).

Answer 'L' for long options (those with two dash e.g. : "--help").

Answer 'D' for a block of descriptions.

• Could I enter specific delimiters to parse my output ?

Of course, just add '-rs "your record separator regexp"' and/or '-fs "your field separator regexp"'. Two type of delimiters: RS and FS. There are the same as RS and FS in awk language.

• What are other options (disp, ga2p, p2ga) ?

It is just to display the content of a galaxy workflow (disp) or for Pise users who would like to convert a Galaxy Workflow into a Pise wrapper (not working for the moment).

Copyright 2014 Dernat Rémy

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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