Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter?
I'm using this as my tool description right now:
<tool id="subsample_fastq" name="Random subsample"> <description>a fastq file</description> <command> ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if </command> <inputs> <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of Pair)"/> <param name="fq2" type="data" format="fastq" label="FASTQ file (2nd of Pair)" optional="true"/> <param name="readsRequested" type="integer" min="1" value="100000" label="Total number of reads you want from the file"/> </inputs> <outputs> <data format="fastq" name="out1" /> <data format="fastq" name="out2" /> </outputs> <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>