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
Thanks
Neil
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