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>
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