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...
> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
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