Re: [galaxy-dev] optional tool arguments
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 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 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: >>> >>> >>> a fastq file >>> >>> ### 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 $out1 >>> #end if >>> >>> >>> >>> >>> >> label="Total number of reads you want from the file"/> >>> >>> >>> >>> >>> >>> >>> >> /> >>> >>> >>> >>> >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] optional tool arguments
Yes, for example: https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml Peter On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz wrote: > Hi Ryan > > I guess you can work with filters, see: > > https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set > > > > Regards, Hans-Rudolf > > > > > On 04/28/2015 06:28 PM, Ryan G wrote: >> >> Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or >> 2 fastq files as input. If 1 file is specified, then 1 output file is >> created. If 2 inputs are specified, then 2 output files will be >> created. How do I specify the optional output parameter? >> >> I'm using this as my tool description right now: >> >> >>a fastq file >> >> ### Check for optional input file >> #if strlen($fq2) > 0: >>RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o >> $out2 >> #else: >>RandomSubFq -w $readsRequested -i "$fq1" -o $out1 >> #end if >> >> >> >> >> > label="Total number of reads you want from the file"/> >> >> >> >> >> >> >> > /> >> >> >> >> >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >>https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] optional tool arguments
Hi Ryan I guess you can work with filters, see: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set Regards, Hans-Rudolf On 04/28/2015 06:28 PM, Ryan G wrote: Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or 2 fastq files as input. If 1 file is specified, then 1 output file is created. If 2 inputs are specified, then 2 output files will be created. How do I specify the optional output parameter? I'm using this as my tool description right now: a fastq file ### Check for optional input file #if strlen($fq2) > 0: RandomSubFq -w $readsRequested -i "$fq1" -i "$fq2" -o $out1 -o $out2 #else: RandomSubFq -w $readsRequested -i "$fq1" -o $out1 #end if ___ 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/
