Hi,

I am trying to integrate some tools into Galaxy but I have encountered some difficulties in attempting to understand how the XML tool definition works exactly ... despite the XML tag documentation available at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax .

Imagine a case where the presence of certain arguments depends on:

- its value e.g we don't want to include it if its value is undefined

  - other arguments' values e.g if the value of x is greater than the y value we don't want to include the x argument on the command line 

How can I specify it using the XML definition?

A simplified case:

A tool needs arguments A and B or an input file F

We want to propose two modes to configure it 

- [1] a basic mode where we can graphically set A and B values using fields such as text value...

- [2] an advanced mode where we can specify a file containing complex configuration to upload 

tool command line: 

for [1] tool.py -A arg1 -B arg2 

   [2] tool.py -F confile

I don't want to include the -F command line argument if -A and -B are defined

I currently manage these cases using wrappers...quite boring  

Where can we find: 

       - advanced documentation for XML definition

       - commented advanced examples 

       - related discussions 

Best regards

Seb 

[sorry for the bad english]