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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