Hi Sébastien,
You can use regular Cheetah syntax in our xml configs, like such:
#if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
#else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
#end if
The above was extracted from the wiki page you linked, although we don't seem to have explicit Cheetah definitions
-Kanwei
2010/7/9 Sébastien HARISPE harispe.sebastien@gmail.com:
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] _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev