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 

my xml file looks like this:
<tool id="reorient_studies" name="Reorient images">
  <description>for CTE surface</description>
  <!-- <command 
 $input $installDir $outputDir ${os.path.join( input.extra_files_path, 
'%s.nii.gz' % input.metadata.base_name )} -->
 $input $installDir $outputDir
    <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" />
    <data format="input" name="output_mvb" from_work_dir="temp.mvb" />

(mvb is a new datatype i've added)

datatypes_conf.xml :

<datatype extension="mvb" type="galaxy.datatypes.data:Mvb" 

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'
    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


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