Hi Ryan

I guess you can work with filters, see:

https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set



Regards, Hans-Rudolf



On 04/28/2015 06:28 PM, Ryan G wrote:
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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