Hi,
I think I found the solution to my problem by googling it instead of just
searching through the dev mailing list. I found this post very useful for
debugging tips on cheetah template:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004817.html
Then I read on the galaxy wiki:
http://wiki.g2.bx.psu.edu/Admin/Tools/Data%20Tables How to use Data Tables and
found this:
"""
The script or binary will need the actual path in the command, and since the ID
is the value, some work will need to be done to extract the path. The following
line would do the trick: --ref="${ filter( lambda x: str( x[0] ) == str( $index
), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" In
this line, str( x[0] ) refers to the unique ID in column 0 and the -1 in
[0][-1] gets the path in the last column.
"""
I've changed the command to print all available parameters:
#silent sys.stderr.write(" Cheetah Template Variables \n")
#for k,v in $searchList[2].items()
#silent sys.stderr.write(" %s = %s\n" % (str(k), str(v) ))
#end for
#silent sys.stderr.write("CRI datasets: %s\n" %
str($__app__.tool_data_tables[ 'cri_datasets' ].get_fields()))
#silent sys.stderr.write("Dataset selected: %s\n" % str($dataset.name))
#silent dataset_path = filter( lambda x: str( x[0] ) == str( $dataset.name ),
$__app__.tool_data_tables[ 'cri_datasets' ].get_fields() )[0][-1]
#silent sys.stderr.write("Dataset path: %s\n" % str(dataset_path) )
#silent sys.stderr.write(" end-of-list \n")
...
and finally got it to works!
To summary, to get the path from the cri_datasets table:
dataset_path = filter( lambda x: str( x[0] ) == str( $dataset.name ),
$__app__.tool_data_tables[ 'cri_datasets' ].get_fields() )[0][-1]
Hope it could be useful to someone else.
Anne.
On 22 May 2012, at 19:52, Anne Pajon wrote:
> Hi,
>
> I'm writing a galaxy tool xml file for an in house existing R script. I have
> a conditional parameter set for selecting the dataset to work with but I
> would like to access the path of the file from the data table I've created:
>
>
> value, name, path
>
>
>
> Here is the beginning of the xml file:
>
>
>rp.R --args $dataset.name.fields.name $dataset.name.fields.path $input
> $column $output_txt $output_html $output_html.files_path $dataset.outcome
> $dataset.receptor $dataset.treatment $dataset.er $dataset.age $dataset.grade
> $dataset.signature $dataset.margins $dataset.groups $dataset.gleason
> $dataset.tstage 2>stderr || cat stderr 1>&2
>
>
>
> help="File containing a list of gene symbols"/>
> label="Column" help="Column containing gene symbols (only available for
> tabular input file)" />
>
>
>
>
>
> ...
>
> but when running the tool, here is the error message I get:
>
> Traceback (most recent call last):
> File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/runners/local.py", line
> 59, in run_job
>job_wrapper.prepare()
> File "/opt/local/home/webapp/galaxy/lib/galaxy/jobs/__init__.py", line 429,
> in prepare
>self.command_line = self.tool.build_command_line( param_dict )
> File "/opt/local/home/webapp/galaxy/lib/galaxy/tools/__init__.py", line
> 1971, in build_command_line
>command_line = fill_template( self.command, context=param_dict )
> File "/opt/local/home/webapp/galaxy/lib/galaxy/util/template.py", line 9, in
> fill_template
>return str( Template( source=template_text, searchList=[context] ) )
> File
> "/opt/local/home/webapp/galaxy/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py",
> line 1004, in __str__
>return getattr(self, mainMethName)()
> File "DynamicallyCompiledCheetahTemplate.py", line 83, in respond
> NotFound: cannot find 'fields' while searching for 'dataset.name.fields.name'
>
> Is it possible to access the other columns of a loc file? It seems possible
> based of what I read on the wiki
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coptions.3E_tag_set
> using from_data_table and syntax of ${param.fields.path} but I could not
> manage to make it work.
>
> Any help would be very much appreciated. Thanks!
> Kind regards,
> Anne.
>
> --
> Anne Pajon, Ph.D.
> Cancer Research UK - Cambridge Research Institute
> Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
> anne.pa...@cancer.org.uk | +44 (0)1223 404 334
>
>
--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cancer.org.uk | +44 (0)1223 404 334
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