Nate is right - full traceback would help. I am not sure it is the
only problem - but these outputs do not look right:

<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>

Galaxy isn't going to expand variables ($Project.input /
$Project.samples) in the from_work_dir attribute so those are going to
be taken as literal strings. That directory also really needs to be
relative to the tool directory and I believe this is enforced for
security reasons.

-John


On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> 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.gruen...@googlemail.com
> <bjoern.gruen...@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
> <martinchristianse...@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.gruen...@gmail.com
>> > To: martinchristianse...@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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