Hi Nicola
Many thanks for your comments/suggestions. I've just tested the rnaStar wrapper, and it works as well.
I will try to dig deeper
Hans-Rudolf
On 08/16/2016 01:38 PM, Nicola Soranzo wrote:
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_rn... 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.3E_t... ). I tried the code from the wiki which is based on the bowtie_wrapper (https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrap...) 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
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