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> <inputs> <param name="sPaired" type="boolean" truevalue="paired" falsevalue="single" checked="yes" label="Reads are paired" /> <!--<param name="sPaired" type="select" label="Is this library mate-paired?"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> </param>--> <param name="bam_in" type="data" format="bam" label="BAM File to Convert" /> </inputs> <outputs> <data name="fastq1_out" format="fastqsanger" /> <data name="fastq2_out" format="fastqsanger" > <filter>sPaired == "paired"</filter> </data> </outputs> <tests> </tests> <help> </help> </tool> Regards 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.