Yes it took some experimenting but I finally figured it out. Sent from my iPhone
> On Apr 29, 2015, at 4:51 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > > Yes, for example: > https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml > > Peter > >> On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: >> 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> >>> >>> >>> >>> >>> ___________________________________________________________ >>> 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: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
