One follow up question then:
The #if#else syntax, in for example this tool example:
...
<command interpreter="python">
sam_to_bam.py
--input1=$source.input1
--dbkey=${input1.metadata.dbkey}
#if $source.index_source == "history":
--ref_file=$source.ref_file
#else
--ref_file="None"
#end if
--output1=$output1
--index_dir=${GALAXY_DATA_INDEX_DIR}
</command>
<inputs>
...
... is that something that you galaxy parses itself (tried to grep for
some matching-code, but found nothing so far), or are that some python
preprocessor directives?
Best
// Samuel
On 07/22/2011 04:45 PM, Samuel Lampa wrote:
Ah, thanks! I somehow missed that file altogether ...
// Samuel
On 07/22/2011 03:59 PM, Greg Von Kuster wrote:
Samuel,
Look at the parse(0 method in the Tool class in
~/lib/galaxy/tools/__init__.py for most of it. You should be able to
find everything you need from there.
Greg Von Kuster
On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote:
Quick question to you devs,
I need to find the code where the tool configs are parsed ...
especially the "free-text" if-else clauses in the command-tag.
Could someone point me to the file?
TIA
// Samuel
--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--------------------------------------
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se
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Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
--
System Expert / Bioinformatician
SNIC-UPPMAX / SciLifeLab Uppsala
Uppsala University, Sweden
--------------------------------------
E-mail: samuel.la...@scilifelab.uu.se
Phone: +46 (0)18 - 471 1060
WWW: http://www.uppmax.uu.se
Uppnex: https://www.uppnex.uu.se
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
