On Oct 2, 2012, at 11:44 PM, <neil.burd...@csiro.au> <neil.burd...@csiro.au> 
wrote:

> Hi,
>   I was under the impression that when a composite datatype (basic) file is 
> uploaded then the files contained within the composite file are also uploaded 
> is this not the case?
> 
> I was hoping my script would be able to have a file as an input. The file 
> contains multiple files. Each one would then be examined and outputted in 
> turn...
> 
> my xml file looks like this:
> <tool id="reorient_studies" name="Reorient images">
>  <description>for CTE surface</description>
>  <!-- <command 
> interpreter="bash">/usr/local/MILXView.12.08.2/BashScripts/CTESurface/tools/reorient_studies.sh
>  $input $installDir $outputDir ${os.path.join( input.extra_files_path, 
> '%s.nii.gz' % input.metadata.base_name )} -->
>  <command 
> interpreter="bash">/usr/local/MILXView.12.08.2/BashScripts/CTESurface/tools/reorient_studies.sh
>  $input $installDir $outputDir
>  </command>
>  <inputs>
>    <param format="mvb" name="input" type="data" label="Input File" />
>    <param type="text" name="installDir" value="/usr/local/MILXView.12.08.2/" 
> label="Atlas" />
>    <param type="text" name="outputDir" value="CTE_SURFACE/" label="White 
> Matter" />
>  </inputs>
>  <outputs>
>    <data format="input" name="output_mvb" from_work_dir="temp.mvb" />
>  </outputs>
> 
> (mvb is a new datatype i've added)
> 
> datatypes_conf.xml :
> 
> <datatype extension="mvb" type="galaxy.datatypes.data:Mvb" 
> display_in_upload="true"/>
> 
> data.py :
> 
> class Mvb( Text ):
>    MetadataElement( name="base_name", desc="base name for all transformed 
> versions of this genetic dataset", readonly=True, set_in_upload=True)
>    composite_type = 'basic'
>    file_ext="mvb"
>    allow_datatype_change = False
> 
>    def __init__( self, **kwd ):
>        Text.__init__( self, **kwd )
>        #self.add_composite_file( '215_T1_MRI_biasCorr.nii.gz', is_binary = 
> True )
>        #self.add_composite_file( 'VOTE_215_T1_MRI_hard_csf.nii.gz', is_binary 
> = True )
>        self.add_composite_file( '%s.nii.gz', description = 'Input File', 
> substitute_name_with_metadata = 'base_name', is_binary = True )
> 
> However, when I uploaded my backup.mvb file. It uploads the file and 
> contents, but doesn't upload the files listed in the *.mvb file. Should it do 
> this? Otherwise why have a composite datatype, as in this case it's simply 
> acting like a text file

Hi Neil,

Is the mvb file some sort of container that actually contains multiple files in 
one file?  This isn't quite how composite datasets work.  In Galaxy, a 
composite dataset is multiple different files on disk that are referred to as a 
single dataset.

--nate

> 
> Thanks
> Neil
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to