> Hi!
>
> I have a tool with three possible types of input. A flag is set to
> either 'bed', 'resource' or 'file' for the two inputs. I've noticed
> that the conditional variables are not available on the command line,
> so is there some other way of setting these flags?
>
> So far, the UI handles the 3 possible input types nicely, but I'd
> like to set the format1 and format2 flags directly from the
> conditional. It seems that the conditional parameters aren't seen by
> cheetah. I also tried using 'hidden' parameters, but those seem to
> be for totally different uses. # USAGE: # python
> enrichment_pairwise.py myfile.bed geneExons --format1=bed
> --format2=resource --genome_resource=hg18 --output_file=overlap.txt
>
> Trying to run this in galaxy gives: Traceback (most recent call
> last): File
> "/home/wbiesing/galaxy_dist/lib/galaxy/jobs/runners/local.py", line
> 55, in run_job job_wrapper.prepare() File
> "/home/wbiesing/galaxy_dist/lib/galaxy/jobs/__init__.py", line 355,
> in prepare self.command_line = self.tool.build_command_line(
> param_dict ) File
> "/home/wbiesing/galaxy_dist/lib/galaxy/tools/__init__.py", line 1397,
> in build_command_line command_line = fill_template( self.command,
> context=param_dict ) File
> "/home/wbiesing/galaxy_dist/lib/galaxy/util/template.py", line 9, in
> fill_template return str( Template( source=template_text,
> searchList=[context] ) ) File
> "/home/wbiesing/galaxy_dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py",
>
>
line 1004, in __str__
> return getattr(self, mainMethName)() File
> "cheetah_DynamicallyCompiledCheetahTemplate_1280646041_98_13115.py",
> line 89, in respond NotFound: cannot find 'res1_select
>
>
> My tool's XML file looks like:
>
> <command interpreter="python">enrichment_pairwise.py $resource1
> $resource2 --format1=$res1_select --format2=$res2_select
> --genome_resource=$dbkey --output_file=$outputFile</command>
> <inputs> <conditional name="resource1_test"> <param
> name="res1_select" type="select" label="Input type for resource1">
> <option value="bed">BED File</option> <option
> value="resource">Worldbase Resource</option> <option
> value="file">File with list of Worldbase Resources</option> </param>
> <when value="bed"> <param name="resource1" type="data" format="bed"
> label="Bed file for resource1" /> </when> <when value="resource">
> <param name="resource1" type="text" label="Worldbase ID for
> resource1" /> </when> <when value="file"> <param name="resource1"
> type="data" format="text" label="Text file with Worldbase IDs to
> iterate over for resource1" /> </when> </conditional>
>
> <conditional name="resource2_test"> <param name="res2_select"
> type="select" label="Input type for resource2"> <option
> value="bed">BED File</option> <option value="resource">Worldbase
> Resource</option> <option value="file">File with list of Worldbase
> Resources</option> </param> <when value="bed"> <param
> name="resource2" type="data" format="bed" label="Bed file for
> resource2" /> </when> <when value="resource"> <param name="resource2"
> type="text" label="Worldbase ID for resource2" /> </when> <when
> value="file"> <param name="resource2" type="data" format="text"
> label="Text file with Worldbase IDs to iterate over for resource2"
> /> </when> </conditional> </inputs>
>
> Thanks for your help! -- Jake Biesinger Graduate Student Xie Lab, UC
> Irvine (949) 231-7587
>
>
>
>