comparison rsem.py @ 1:1ff2fc8da328

Updates to rsem_calculate_expression.xml

0:64d45f959303

"""
SnpEff datatypes
"""
import os,os.path,re,sys
import galaxy.datatypes.data
from galaxy.datatypes.images import Html
from galaxy.datatypes.metadata import MetadataElement

class RsemReference( Html ):
    """Class describing an RSEM reference"""
    MetadataElement( name='reference_name', default='galaxy_generated_bowtie_index', desc='RSEM Reference Name', readonly=True, visible=True, no_value=None )

    file_ext = 'rsem_ref'
    is_binary = True
    composite_type = 'auto_primary_file'
    allow_datatype_change = False

        extra_files_path/<reference_name>.2.ebwt
        extra_files_path/<reference_name>.1.ebwt
        extra_files_path/<reference_name>.rev.2.ebwt
        extra_files_path/<reference_name>.rev.1.ebwt
        """
        log.info( "RSEM reference set_meta %s %s" % (dataset,dataset.extra_files_path))
        pat = '^(.*)\.grp$'
        efp = dataset.extra_files_path
        flist = os.listdir(efp)
        for i,fname in enumerate(flist):
          m = re.match(pat,fname)

1:1ff2fc8da328

"""
RSEM datatypes
"""
import os,os.path,re,sys
import galaxy.datatypes.data
from galaxy.datatypes.images import Html
from galaxy.datatypes.metadata import MetadataElement

class RsemReference( Html ):
    """Class describing an RSEM reference"""
    MetadataElement( name='reference_name', default=None, desc='RSEM Reference Name', readonly=True, visible=True, no_value=None )

    file_ext = 'rsem_ref'
    is_binary = True
    composite_type = 'auto_primary_file'
    allow_datatype_change = False

        extra_files_path/<reference_name>.2.ebwt
        extra_files_path/<reference_name>.1.ebwt
        extra_files_path/<reference_name>.rev.2.ebwt
        extra_files_path/<reference_name>.rev.1.ebwt
        """
        pat = '^(.*)\.grp$'
        efp = dataset.extra_files_path
        flist = os.listdir(efp)
        for i,fname in enumerate(flist):
          m = re.match(pat,fname)