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]