Hi,

Thanks for your reply Li, I was under the impression that Cheetah syntax was reserved for conditional parameters use.

Cheetah is not really simple to debug (Tricks ?).

Can someone help me with the following command definition ?

  <command interpreter="python">
  #set $cmd = ''
  #if $chromo != ''
  #$cmd = ' $cmd -c $chromo '
  #end if
  #if $start != ''
  #$cmd = ' $cmd -s $chromo '
  #end if
  #if $end != ''
  #$cmd = ' $cmd -e $end '
  #end if
  #if $DB != ''
  #$cmd = ' $cmd -d $DB '
  #end if
  #if $conf_file != ''
  #$cmd = ' $cmd -f $conf_file ' 
  #end if
  # ucsc.py  $cmd -o $out -l $log -p $log_C -f  -u $useConf
  </command> 

    

Error:

/usr/bin/python: can't find '__main__.py' in '/xxxxx/galaxy/galaxy_dist/tools/'

Is there a forum or another way to found old related posts ?  

Best regards
 





2010/7/9 Kanwei Li <kanwei@gmail.com>
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]
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>
>