On 15/12/2010 17:23, Peter wrote:
On Wed, Dec 15, 2010 at 5:15 PM, Marina Gourtovaia<mg8@sanger.ac.uk> wrote:
Hello
The boolean widget in the following tool config always works as if not ticked while the select drop-down box in the same situation (teh commented out xml) works ok. What's wrong with my tickbox?
<tool id="bam_to_fastq" name="BAM-to-FASTQ" version="1.0.0"> <requirements> <requirement type="package">picard</requirement> </requirements> <description>converts BAM format to FASTQ format</description> <command> java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/SamToFastq.jar VALIDATION_STRINGENCY=SILENT QUIET=true INPUT=$bam_in FASTQ=$fastq1_out #if $sPaired == "paired": SECOND_END_FASTQ=$fastq2_out #end if </command> Just a guess, but have you tried this - based on similar issues I had writing the NCBI BLAST+ wrappers:
#if str($sPaired) == "paired": SECOND_END_FASTQ=$fastq2_out #end if
The sPaired object isn't actually a string, its a proxy object with the __str__ method defined.
Peter
Thanks a lot for the tip, Peter. Also, had to use a different filter expression (sPaired is True) BTW, I am making a wrapper around Picard http://picard.sourceforge.net/command-line-overview.shtml#Overview. Is there enough interest to this to submit this to the core Galaxy? In Sanger, our Illumina pipeline end up with BAM files, so the end users need a BAM-FASTQ converter, hence this binding I am making Marina Gourtovaia -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.