Hi Martin, If there's a full traceback instead of just this fragment, that'd certainly help with determining exactly where the problem is coming from. --nate On Aug 12, 2014, at 4:17 AM, bjoern.gruening@googlemail.com <bjoern.gruening@gmail.com> wrote:
Hi,
Galaxy stores all information about a tool and it's parameters in a database. I suppose if something is wrong with your tool, under some circumstances, it can't be stored in the database.
Cheers, Bjoern
2014-08-12 9:23 GMT+02:00 Martin Christiansen <martinchristiansendk@hotmail.com>: Hi Björn,
I'm using galaxy as a front-end to run a larger pipeline in the background. Originally I implemented the pipeline which had the same wrapper and was running fine. I have now begun to break it down into steps where this is the first step.
The only thing I've changed is the output. How would this cause an error in the python egg?
Martin
Date: Tue, 12 Aug 2014 09:06:51 +0200 From: bjoern.gruening@gmail.com To: martinchristiansendk@hotmail.com; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] TypeError with 'dict'
Hi Martin,
please keep galaxy-dev in the CC list.
Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
Hi Björn,
Most certainly. I have posted it below.
<tool id="screen_reads" name="Screen Reads">
-> add here a version number version="0.1"
<description>against hg19</description>
<command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command>
<inputs> <conditional name="Project"> <param name="input" type="select" label="Select project"> <option value="galaxy_test1">galaxy_test1</option> <option value="Untitled Folder">Untitled Folder</option>
-> is the white space really needed? If so $Project.input will be two words. Use "${Project.input}" to convert it to onw argument
</param> <when value="galaxy_test1"> <param name="samples" type="select" label="Select samples" display="checkboxes" multiple="True"> <option value="147406386-700171390">147406386-700171390</option> <option value="158256496-700097688">158256496-700097688</option> <option value="158337416-700013715">158337416-700013715</option> <option value="158337416-700097837">158337416-700097837</option> <option value="158357646-700035237">158357646-700035237</option> <option value="158458797-700014562">158458797-700014562</option> <option value="158479027-700014724">158479027-700014724</option> <option value="158479027-700097196">158479027-700097196</option> <option value="158499257-700014837">158499257-700014837</option> <option value="158499257-700098561">158499257-700098561</option> <option value="158742018-700015181">158742018-700015181</option> <option value="158802708-700015245">158802708-700015245</option> <option value="158802708-700015250">158802708-700015250</option> <option value="158802708-700099803">158802708-700099803</option> <option value="158802708-700119165">158802708-700119165</option> <option value="158822939-700014954">158822939-700014954</option> <option value="158883629-700015113">158883629-700015113</option> <option value="158883629-700100227">158883629-700100227</option> <option value="158883629-700112812">158883629-700112812</option> <option value="158924089-700099307">158924089-700099307</option> </param> </when> <when value="Untitled Folder"> <param name="samples" type="select" label="Select samples" display="checkboxes" multiple="True">
-> you don't have any <option> here.
</param> </when> </conditional> </inputs>
<outputs> <data format="tabular" name="Project" label="Project" from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input"/> <data format="tabular" name="Samples" label="Samples" from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples"/> </outputs>
-> I'm not sure this will work. workdir is a special dir Galaxy creates for you. It will be the working directory where your program get's called. So assume your program creates foo.sam files. You can specify it like from_work_dir='foo.sam'
The input handling looks also a little bit strange. You do not specify any input file in Galaxy. That is not really Galaxy like :)
Cheers, Bjoern
<help> Reads screened against hg19. </help> </tool>
Best, Martin
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