Re: [galaxy-dev] problems with 'action type="metadata" name="dbkey"' in tool xml

I've tested bowtie_wrapper on Galaxy release_16.04: <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> works fine for me. Cheers, Nicola On 16/08/16 11:42, Nicola Soranzo wrote: > Forget about my previous comment, I should have read your email > better, sorry! > > Your code similar to bowtie_wrapper is also used by > https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg... > and I think it should work, not sure if it's a regression in Galaxy. > > Cheers, > Nicola > > On 16/08/16 11:29, Nicola Soranzo wrote: >> Hi Hans, >> see my comment below. >> >> On 16/08/16 09:51, Hans-Rudolf Hotz wrote: >>> Dear All >>> >>> >>> I am trying to move our Galaxy installation to new hardware and at >>> the same time to a new version (the original is "15.10",minor >>> version "2" via mercurial; the new is "16.04" via github): >>> >>> So far, I am making good progress, but I am struggling with a tool >>> which was written by someone else who has left more than 2 years >>> ago. The problem is: it doesn't set the dbkey correctly. >>> >>> I get: >>> <Cheetah.Template.Template object at 0x7f1e40210f50> >>> >>> >>> >>> The tool xml is as follows: >>> >>> <inputs> >>> <param name="sample_file" type="data" >>> format="qsamples,qsamplespaired" label="Sample File" help="set of >>> sequence files created by the 'select sequence files' tool"> >>> </param> >>> <param name="index" type="select" label="Reference Genome" >>> help="all reads will be mapped to this reference"> >>> <options from_data_table="fmi__quasr_genomes"/> >>> </param> >>> >>> ... >>> </inputs> >>> <outputs> >>> <data name="output01" type="data" format="qproject" >>> label="qProject of ${sample_file.name}"> >>> <actions> >>> <action type="metadata" name="dbkey"> >>> <option type="from_param" name="index"/> >> >> It seems you are missing a param_attribute="dbkey" here, it should be: >> <option type="from_param" name="index" param_attribute="dbkey"/> >> >> Cheers, >> Nicola >> >>> </action> >>> </actions> >>> </data> >>> </outputs> >>> >>> >>> >>> The user can select a genome (based on the Bioconductor BSgenome >>> packages) from the tab delimited fmi__quasr_genomes table, which >>> looks like: >>> >>> hg19BSg hg19BSg BSgenome Hsapiens (UCSC hg19) >>> BSgenome.Hsapiens.UCSC.hg19 >>> hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18) >>> BSgenome.Hsapiens.UCSC.hg18 >>> ce10BSg ce10BSg BSgenome Celegans (UCSC ce10) >>> BSgenome.Celegans.UCSC.ce10 >>> ce6BSg ce6BSg BSgenome Celegans (UCSC ce6) >>> BSgenome.Celegans.UCSC.ce6 >>> ... >>> >>> >>> The tool works: >>> - it displays the available genomes (BSgenome Hsapiens (UCSC hg19), >>> hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc) >>> - once the job is submitted, it uses the right Bioconductor package >>> (BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc) >>> >>> However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get: >>> <Cheetah.Template.Template object at 0x7f1e40210f50> >>> >>> >>> >>> Has anything changed with the 'action' tag since release 15.10? >>> which makes this simple xml no longer working? >>> >>> I have to admit, it does look different than the example on the wiki >>> (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3... >>> ). I tried the code from the wiki which is based on the >>> bowtie_wrapper >>> (https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_w...) >>> as well: >>> >>> >>> <actions> >>> <action type="metadata" name="dbkey"> >>> <option type="from_data_table" name="fmi__quasr_genomes" >>> column="1" offset="0"> >>> <filter type="param_value" column="0" value="#" >>> compare="startswith" keep="False"/> >>> <filter type="param_value" ref="index" column="0"/> >>> </option> >>> </action> >>> </actions> >>> >>> >>> but it results in the same kind of error: >>> <Cheetah.Template.Template object at 0x7ff82c0e43d0> >>> >>> >>> Thank you very much for any help/comments >>> >>> Regards, Hans-Rudolf >>> >>> >>> >>> >>> >>> >>> >> >> ___________________________________________________________ >> 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/