Hi Nicola and others on the list

It looks like it has something to do with the 'conditional'

I took the rnaStar xml file, and reduced it to the bare bones, just to reproduce the issue (see attachment: rg_rnaStar.simple ). This works. It picks up the right dbkey.

I made the xml file even simpler and removed the 'conditional' (see attachment: rg_rnaStar.simple_noCond ). And now it no longer works (see attached screenshot)

And just for completeness: There is nothing in the logs


However, if I use the same two xml files on our current galaxy servers (running 15.10). It works in both cases. Each time, the right dbkey is picked up.


 Hans-Rudolf



On 08/16/2016 01:47 PM, Hans-Rudolf Hotz wrote:
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_rnaStar.xml

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_tag_set

). I tried the code from the wiki which is based on the
bowtie_wrapper
(https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml)

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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<tool id="rna_star" name="RNA STAR" version="500">
    <description>Gapped-read mapper for RNA-seq data</description>
    <command>echo foo > $mapped_reads
</command>

    <inputs>
    
        <!-- Genome source. -->
        <conditional name="refGenomeSource">
            <param name="genomeSource" type="select" label="Custom or built-in 
reference genome" help="Built-ins were indexed using default options">
                <option value="indexed" selected="True">Use a built-in 
index</option>
                <option value="history">Index and use a genome fasta and GTF 
file from history</option>
            </param>
            <when value="indexed">
            <param name="index" type="select" label="Select a reference genome">
                <options from_data_table="fmi__quasr_genomes">
                    <filter type="sort_by" column="2"/>
                    <validator type="no_options" message="No indexes are 
available for the selected input dataset"/>
                </options>
            </param>
            </when>
            <when value="history">
                <param name="ownFile" type="data" format="fasta" 
metadata_name="dbkey" label="Select the reference genome" />
                <param name="geneModel" type="data" format="gff3,gtf" 
label="Gene model (gff3,gtf) file for splice junctions. Leave blank for none"
                    optional="true" help="Optional. If supplied, the index file 
will retain exon junction information for mapping splices (--sjdbGTFfile)"/>
                <param name="overhang" type="integer" min="0" value="100" 
label="Length of the genomic sequence around annotated junctions" help="Used in 
constructing the splice junctions database. Ideal value is ReadLength-1 
(--sjdbOverhang)"/>
            </when>
        </conditional>
        

        
    </inputs>

    <outputs>

        
        <data format="txt" name="mapped_reads">
            <actions>
                <conditional name="refGenomeSource.genomeSource">
                    <when value="indexed">
                        <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="refGenomeSource.index" column="0"/>
                            </option>
                        </action>
                    </when>
                    <when value="history">
                        <action type="metadata" name="dbkey">
                            <option type="from_param" 
name="refGenomeSource.ownFile" param_attribute="dbkey" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
    </outputs>


    <help>
**What it does**

</help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/bts635</citation>
    </citations>
</tool>
<tool id="rna_star" name="RNA STAR no Cond" version="501">
    <description>Gapped-read mapper for RNA-seq data</description>
    <command>echo foo > $mapped_reads
</command>

    <inputs>
    
        <!-- Genome source. --> 
            <param name="index" type="select" label="Select a reference genome">
                <options from_data_table="fmi__quasr_genomes">
                    <filter type="sort_by" column="2"/>
                    <validator type="no_options" message="No indexes are 
available for the selected input dataset"/>
                </options>
            </param>

    
        
    </inputs>

    <outputs>

        
        <data format="txt" name="mapped_reads">
            <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>
        </data>
    </outputs>


    <help>
**What it does**

</help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/bts635</citation>
    </citations>
</tool>
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