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>
    ### Check for optional input file
    #if strlen($fq2) > 0:
      RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2
      RandomSubFq -w $readsRequested -i "$fq1" -o $out1
    #end if
    <param name="fq1" type="data" format="fastq" label="FASTQ file (1st of
    <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"/>
    <data format="fastq" name="out1" />
    <data format="fastq" name="out2" />
    <exit_code range="-1" level="fatal" description="RandomSubFq failed" />
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

To search Galaxy mailing lists use the unified search at:

Reply via email to