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.lampa@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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-- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa@scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se