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Modified all tools to use the new <options> tag for dynamic select lists. Completely eliminated the <select_options> tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py.

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This commit is contained in:
Greg Von Kuster
2007-11-29 17:04:42 +00:00
parent 2a6cb86131
commit 79745f4012
19 changed files with 395 additions and 386 deletions
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lib/galaxy/tools/dynamic_options.py
+209 -203
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@@ -6,6 +6,7 @@ log = logging.getLogger(__name__)
class DynamicOptions( object ):
"""Handles dynamically generated SelectToolParameter options"""
def __init__( self, elem ):
self.from_file_data = None
# FIXME: Pushing these things in as options ends up being pretty ugly.
# We should find a way to make this work through the validation mechanism.
self.no_data_option = [ ( 'No data available for this build', 'None', True ) ]
@@ -23,28 +24,20 @@ class DynamicOptions( object ):
except:
self.data_file = self.from_file
else: self.data_file = None
if elem.tag == 'select_options':
self.data_ref = elem.get( 'data_ref', None )
self.param_ref = elem.get( 'param_ref', None )
self.func = elem.get( 'func', None )
assert self.func is not None, "Value for option generator function not found"
self.func_params = elem.findall( 'func_param' )
else: #elem.tag =='options'
self.filters = elem.findall( 'filter' )
self.data_ref = None
for filter in self.filters:
filter_type = filter.get( 'type', None )
assert filter_type is not None, "Required 'type' attribute missing from filter"
if filter_type.strip() == 'data_meta':
self.data_ref = filter.get( 'data_ref', None )
assert self.data_ref is not None, "Required 'data_ref' attribute missing from 'data_meta' filter"
self.data_ref = self.data_ref.strip()
elif filter_type.strip() == 'param_meta':
self.param_ref = filter.get( 'param_ref', None )
assert self.param_ref is not None, "Required 'param_ref' attribute missing from 'param_meta' filter"
self.param_ref = self.param_ref.strip()
#FIXME: this attr is used only by microbial import, so shouldn't be at this level
self.microbe_info = None
self.tool_type = elem.get( 'tool_type', None )
self.filters = elem.findall( 'filter' )
self.data_ref = None
for filter in self.filters:
filter_type = filter.get( 'type', None )
assert filter_type is not None, "Required 'type' attribute missing from filter"
if filter_type.strip() == 'data_meta':
self.data_ref = filter.get( 'data_ref', None )
assert self.data_ref is not None, "Required 'data_ref' attribute missing from 'data_meta' filter"
self.data_ref = self.data_ref.strip()
elif filter_type.strip() == 'param_meta':
self.param_ref = filter.get( 'param_ref', None )
assert self.param_ref is not None, "Required 'param_ref' attribute missing from 'param_meta' filter"
self.param_ref = self.param_ref.strip()
def get_dataset( self, trans, other_values ):
# No value indicates a configuration error, the named DataToolParameter must preceed this parameter in the tool config
assert self.data_ref in other_values, "Value for associated DataToolParameter not found"
@@ -56,14 +49,18 @@ class DynamicOptions( object ):
# Currently dynamically generated select lists do not work well with optional datasets.
return None
return dataset
def get_param_value( self, trans, other_values ):
def get_param_value( self, param, trans, other_values ):
if param is None: return None
assert param in other_values, "Value for associated param_value %s not found" %param
return other_values[ param ]
def get_param_ref_value( self, trans, other_values ):
if self.param_ref is None: return None
assert self.param_ref in other_values, "Value for associated parameter %s not found" %self.param_ref.name
assert self.param_ref in other_values, "Value for associated param_ref %s not found" %self.param_ref.name
return other_values[ self.param_ref ]
def get_unique_elems( self, elems ):
seen = set()
return [ x for x in elems if x not in seen and not seen.add( x ) ]
def get_options( self, trans, other_values, must_be_valid = False ):
def get_options( self, trans, other_values, must_be_valid=False ):
filters = {}
key = None
# Check for filters and build a dictionary from them
@@ -84,7 +81,6 @@ class DynamicOptions( object ):
if key == 'build': value = dataset.get_dbkey()
elif key == 'file_name': value = dataset.get_file_name()
elif key == 'species': value = dataset.metadata.species
elif key == 'maf': pass # value does not need to be set, maf tools require special handling - see below
filters[ 'data_meta' ][ 'value' ] = value
if self.data_file == 'maf_index.loc' and key == 'build' and value == '?':
if must_be_valid: return []
@@ -94,8 +90,20 @@ class DynamicOptions( object ):
key = filter.get( 'key', None )
assert key is not None, "key attribute missing from param_meta filter"
filters[ 'param_meta' ][ 'key' ] = key.strip()
value = self.get_param_value( trans, other_values )
value = self.get_param_ref_value( trans, other_values )
filters[ 'param_meta' ][ 'value' ] = value
elif filter_type == 'param_value':
n = filter.get( 'name', None )
assert n is not None, "param_value filters require a 'name' attribute"
n = n.strip()
v = self.get_param_value( n, trans, other_values )
assert v is not None, "param_value filters require a 'value' attribute"
v = v.strip()
try:
filters[ 'param_values' ][ n ] = v
except:
filters[ 'param_values' ] = {}
filters[ 'param_values' ][ n ] = v
elif filter_type == 'column':
n = filter.get( 'name', None )
assert n is not None, "column filters require a 'name' attribute"
@@ -109,7 +117,6 @@ class DynamicOptions( object ):
filters[ 'columns' ] = {}
filters[ 'columns' ][ n ] = v
elif filter_type == 'param':
# TODO: I'm not sure I like the way 'param' filters are implemented, I may be rethinking this approach...
n = filter.get( 'name', None )
assert n is not None, "param filters require a 'name' attribute"
n = n.strip()
@@ -121,14 +128,15 @@ class DynamicOptions( object ):
except:
filters[ 'params' ] = {}
filters[ 'params' ][ n ] = v
# Now that we've parsed our filters, we need to see if the tool is a maf tool which requires special handling
# Now that we've parsed our filters, we need to see if the tool is a maf tool
# which requires special handling
try: key = filters[ 'data_meta' ][ 'key' ]
except: key == None
except: key = None
if key == 'maf':
maf_source = filters[ 'params' ][ 'maf_source' ]
if maf_source == 'cached':
maf_uid = filters[ 'param_meta' ][ 'value' ]
if maf_uid in [None, 'None']:
if maf_uid in [ None, 'None' ]:
if must_be_valid: return []
if maf_uid is None: return self.no_data_option
if maf_uid == 'None': return self.build_not_set_option
@@ -137,45 +145,62 @@ class DynamicOptions( object ):
if dataset is None: return self.wait_for_maf_option
filters[ 'data_meta' ][ 'key' ] = 'species'
filters[ 'data_meta' ][ 'value' ] = dataset.metadata.species
return self.generate_options( filters, must_be_valid = must_be_valid )
def generate_options( self, filters={}, sep='\t', must_be_valid = False ):
# Extract the info from the tool's options filters, if any
try: key = filters[ 'data_meta' ][ 'key' ]
except: key = None
try: value = filters[ 'data_meta' ][ 'value' ]
except: value = None
if key is None and value is None:
# Look for param_meta filter
try: key = filters[ 'param_meta' ][ 'key' ]
except: key = None
try: value = filters[ 'param_meta' ][ 'value' ]
except: value = None
try: name_col = int( filters[ 'columns' ][ 'name_col' ] )
except: name_col = None
try: value_col = int( filters[ 'columns' ][ 'value_col' ] )
except: value_col = None
try: encode_group = filters[ 'params' ][ 'encode_group' ]
except: encode_group = None
try: build = filters[ 'params' ][ 'build' ]
except: build = None
try: maf_source = filters[ 'params' ][ 'maf_source' ]
except: maf_source = None
# Order of the following conditionals is critical
if encode_group is not None and build is not None:
return self.generate_from_file_for_encode( encode_group, build, must_be_valid = must_be_valid )
elif key == 'species':
return self.generate_from_dataset_for_species( value )
elif key == 'maf':
return self.generate_from_file_for_maf( maf_source, value, must_be_valid = must_be_valid )
elif key == 'file_name':
return self.generate_from_dataset( value, value_col )
elif key == 'build':
build_col = int( filters[ 'columns' ][ 'build_col' ].strip() )
return self.generate_from_file_for_build( value, build_col, name_col, value_col, must_be_valid = must_be_valid )
elif key is None:
return self.generate_from_file( name_col, value_col )
def generate_from_file_for_encode( self, encode_group, build, sep='\t', must_be_valid = False ):
return self.generate_options( filters, must_be_valid=must_be_valid )
def generate_options( self, filters={}, sep='\t', must_be_valid=False ):
if self.tool_type == 'upload':
return self.generate_from_datatypes_registry()
elif self.tool_type == 'encode':
encode_group = filters[ 'params' ][ 'encode_group' ]
build = filters[ 'params' ][ 'build' ]
return self.generate_from_file_for_encode( encode_group, build, must_be_valid=must_be_valid )
elif self.tool_type == 'microbial':
if self.from_file_data is None: self.load_microbial_data()
try: kingdom = filters[ 'param_values' ][ 'kingdom' ]
except: kingdom = None
try: org = filters[ 'param_values' ][ 'org' ]
except: org = None
try: feature = filters[ 'params' ][ 'feature' ]
except: feature = None
return self.generate_from_file_for_microbial( kingdom, org, feature, must_be_valid=must_be_valid )
else: # self.tool_type is None
try: key = filters[ 'data_meta' ][ 'key' ]
except:
try: key = filters[ 'param_meta' ][ 'key' ]
except: key = None
if key == 'species':
value = filters[ 'data_meta' ][ 'value' ]
return self.generate_from_dataset_for_species( value )
elif key == 'maf':
maf_source = filters[ 'params' ][ 'maf_source' ]
try: value = filters[ 'data_meta' ][ 'value' ]
except: value = filters[ 'param_meta' ][ 'value' ]
return self.generate_from_file_for_maf( maf_source, value, must_be_valid=must_be_valid )
elif key == 'file_name':
value = filters[ 'data_meta' ][ 'value' ]
value_col = int( filters[ 'columns' ][ 'value_col' ] )
return self.generate_from_dataset( value, value_col )
elif key == 'build':
value = filters[ 'data_meta' ][ 'value' ]
build_col = int( filters[ 'columns' ][ 'build_col' ].strip() )
name_col = int( filters[ 'columns' ][ 'name_col' ] )
value_col = int( filters[ 'columns' ][ 'value_col' ] )
return self.generate_from_file_for_build( value, build_col, name_col, value_col, must_be_valid=must_be_valid )
else: # key is None
name_col = int( filters[ 'columns' ][ 'name_col' ] )
value_col = int( filters[ 'columns' ][ 'value_col' ] )
return self.generate_from_file( name_col, value_col )
def generate_from_datatypes_registry( self ):
from galaxy.datatypes import registry
datatypes_registry = registry.Registry()
options = []
formats = datatypes_registry.datatypes_by_extension.keys()
formats.sort()
options.append( ( 'Auto-detect', 'auto', True ) )
for format in formats:
label = format.capitalize()
options.append( ( label, format, False ) )
return options
def generate_from_file_for_encode( self, encode_group, build, sep='\t', must_be_valid=False ):
options = []
def generate():
encode_sets = {}
@@ -253,12 +278,121 @@ class DynamicOptions( object ):
if must_be_valid: return []
return self.no_data_option_not_selected
return options
def generate_from_file_for_microbial( self, kingdom=None, org=None, feature=None, must_be_valid=False ):
options = []
if not kingdom and not org and not feature:
kingdoms = self.from_file_data.keys()
kingdoms.sort()
for kingdom in kingdoms:
options.append( ( kingdom, kingdom, False ) )
if options:
options[0] = ( options[0][0], options[0][1], True )
elif kingdom and not org and not feature:
orgs = self.from_file_data[ kingdom ].keys()
#need to sort by name
swap_test = False
for i in range( 0, len( orgs ) - 1 ):
for j in range( 0, len( orgs ) - i - 1 ):
if self.from_file_data[ kingdom ][ orgs[ j ] ][ 'name' ] > self.from_file_data[ kingdom ][ orgs[ j + 1 ] ][ 'name' ]:
orgs[ j ], orgs[ j + 1 ] = orgs[ j + 1 ], orgs[ j ]
swap_test = True
if swap_test == False: break
for org in orgs:
if self.from_file_data[ kingdom ][ org ][ 'link_site' ] == "UCSC":
options.append( ( "<b>" + self.from_file_data[ kingdom ][ org ][ 'name' ] + "</b> <a href=\"" + self.from_file_data[ kingdom ][ org ][ 'info_url' ] + "\" target=\"_blank\">(about)</a>", org, False ) )
else:
options.append( ( self.from_file_data[ kingdom ][ org ][ 'name' ] + " <a href=\"" + self.from_file_data[ kingdom ][ org ][ 'info_url' ] + "\" target=\"_blank\">(about)</a>", org, False ) )
if options:
options[0] = ( options[0][0], options[0][1], True)
else:
chroms = self.from_file_data[ kingdom ][ org ][ 'chrs' ].keys()
chroms.sort()
for chr in chroms:
for data in self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'data' ]:
if self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'data' ][ data ][ 'feature' ] == feature:
options.append( ( self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'name' ] + " <a href=\"" + self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'info_url' ] + "\" target=\"_blank\">(about)</a>", data, False ) )
return options
def load_microbial_data( self, sep='\t' ):
microbe_info= {}
orgs = {}
for line in open( self.from_file ):
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#' ):
fields = line.split( sep )
#read each line, if not enough fields, go to next line
try:
info_type = fields.pop(0)
if info_type.upper() == "ORG":
#ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
org_num = fields.pop(0)
name = fields.pop(0)
kingdom = fields.pop(0)
group = fields.pop(0)
chromosomes = fields.pop(0)
info_url = fields.pop(0)
link_site = fields.pop(0)
if org_num not in orgs:
orgs[ org_num ] = {}
orgs[ org_num ][ 'chrs' ] = {}
orgs[ org_num ][ 'name' ] = name
orgs[ org_num ][ 'kingdom' ] = kingdom
orgs[ org_num ][ 'group' ] = group
orgs[ org_num ][ 'chromosomes' ] = chromosomes
orgs[ org_num ][ 'info_url' ] = info_url
orgs[ org_num ][ 'link_site' ] = link_site
elif info_type.upper() == "CHR":
#CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
org_num = fields.pop(0)
chr_acc = fields.pop(0)
name = fields.pop(0)
length = fields.pop(0)
gi = fields.pop(0)
gb = fields.pop(0)
info_url = fields.pop(0)
chr = {}
chr[ 'name' ] = name
chr[ 'length' ] = length
chr[ 'gi' ] = gi
chr[ 'gb' ] = gb
chr[ 'info_url' ] = info_url
if org_num not in orgs:
orgs[ org_num ] = {}
orgs[ org_num ][ 'chrs' ] = {}
orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr
elif info_type.upper() == "DATA":
#DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
uid = fields.pop(0)
org_num = fields.pop(0)
chr_acc = fields.pop(0)
feature = fields.pop(0)
filetype = fields.pop(0)
path = fields.pop(0)
data = {}
data[ 'filetype' ] = filetype
data[ 'path' ] = path
data[ 'feature' ] = feature
if org_num not in orgs:
orgs[ org_num ] = {}
orgs[ org_num ][ 'chrs' ] = {}
if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]:
orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {}
orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data
else: continue
except: continue
for org_num in orgs:
org = orgs[ org_num ]
if org[ 'kingdom' ] not in microbe_info:
microbe_info[ org[ 'kingdom' ] ] = {}
if org_num not in microbe_info[ org[ 'kingdom' ] ]:
microbe_info[ org[ 'kingdom' ] ][org_num] = org
self.from_file_data = microbe_info
def generate_from_dataset_for_species( self, value ):
options = []
for species in value:
options.append( ( species, species, False ) )
return options
def generate_from_file_for_maf( self, maf_source, maf_uid, sep='\t', must_be_valid = False ):
def generate_from_file_for_maf( self, maf_source, maf_uid, sep='\t', must_be_valid=False ):
options = []
d = {}
# We will only reach here if the maf-source param value is 'cached'
@@ -285,7 +419,7 @@ class DynamicOptions( object ):
if must_be_valid: return []
return self.no_data_option
return options
def generate_from_dataset( self, value, value_col, sep='\t', must_be_valid = False ):
def generate_from_dataset( self, value, value_col, sep='\t', must_be_valid=False ):
options = []
elem_list = []
try: in_file = open( value, "r" )
@@ -307,7 +441,7 @@ class DynamicOptions( object ):
for elem in elem_list:
options.append( ( elem, elem, False ) )
return options
def generate_from_file_for_build( self, value, build_col, name_col, value_col, sep='\t', must_be_valid = False ):
def generate_from_file_for_build( self, value, build_col, name_col, value_col, sep='\t', must_be_valid=False ):
options = []
d = {}
for line in open( self.from_file ):
@@ -330,7 +464,7 @@ class DynamicOptions( object ):
if not fields[ build_col ] in d:
d[ fields[ build_col ] ] = []
d[ fields[ build_col ] ].append( (fields[ name_col ], fields[ value_col ]) )
elif self.data_file == 'maf_index.loc':
elif self.data_file == 'maf_index.loc' or self.data_file == 'maf_pairwise.loc':
try:
maf_desc = fields[ name_col ] # ENCODE TBA (hg17)
maf_uid = fields[ value_col ] # ENCODE_TBA_hg17
@@ -359,7 +493,7 @@ class DynamicOptions( object ):
if value in d:
for (key, val) in d[ value ]:
options.append( ( key, val, False ) )
elif self.data_file == 'maf_index.loc':
elif self.data_file == 'maf_index.loc' or self.data_file == 'maf_pairwise.loc':
for key in d:
if value in d[ key ][ 'builds' ]:
options.append( ( d[ key ][ 'description' ], key, False ) )
@@ -379,131 +513,3 @@ class DynamicOptions( object ):
# TODO: this option list should be sorted
options.append( ( fields[ name_col ], fields[ value_col ], False ) )
return options
def load_from_file_for_microbial( self ):
self.from_file = "/depot/data2/galaxy/microbes/microbial_data.loc"
microbe_info= {}
orgs = {}
for line in open( self.from_file ):
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#' ):
fields = line.split( '\t' )
#read each line, if not enough fields, go to next line
try:
info_type = fields.pop(0)
if info_type.upper() == "ORG":
#ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
org_num = fields.pop(0)
name = fields.pop(0)
kingdom = fields.pop(0)
group = fields.pop(0)
chromosomes = fields.pop(0)
info_url = fields.pop(0)
link_site = fields.pop(0)
if org_num not in orgs:
orgs[org_num] = {}
orgs[org_num]['chrs'] = {}
orgs[org_num]['name'] = name
orgs[org_num]['kingdom'] = kingdom
orgs[org_num]['group'] = group
orgs[org_num]['chromosomes'] = chromosomes
orgs[org_num]['info_url'] = info_url
orgs[org_num]['link_site'] = link_site
elif info_type.upper() == "CHR":
#CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
org_num = fields.pop(0)
chr_acc = fields.pop(0)
name = fields.pop(0)
length = fields.pop(0)
gi = fields.pop(0)
gb = fields.pop(0)
info_url = fields.pop(0)
chr = {}
chr['name'] = name
chr['length'] = length
chr['gi'] = gi
chr['gb'] = gb
chr['info_url'] = info_url
if org_num not in orgs:
orgs[org_num] = {}
orgs[org_num]['chrs'] = {}
orgs[org_num]['chrs'][chr_acc] = chr
elif info_type.upper() == "DATA":
#DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
uid = fields.pop(0)
org_num = fields.pop(0)
chr_acc = fields.pop(0)
feature = fields.pop(0)
filetype = fields.pop(0)
path = fields.pop(0)
data = {}
data['filetype'] = filetype
data['path'] = path
data['feature'] = feature
if org_num not in orgs:
orgs[org_num] = {}
orgs[org_num]['chrs'] = {}
if 'data' not in orgs[org_num]['chrs'][chr_acc]:
orgs[org_num]['chrs'][chr_acc]['data'] = {}
orgs[org_num]['chrs'][chr_acc]['data'][uid] = data
else: continue
except: continue
for org_num in orgs:
org = orgs[org_num]
if org['kingdom'] not in microbe_info:
microbe_info[org['kingdom']] = {}
if org_num not in microbe_info[org['kingdom']]:
microbe_info[org['kingdom']][org_num] = org
self.microbe_info = microbe_info
def get_options_for_kingdoms( self, trans, other_values ):
if self.microbe_info == None: self.load_from_file_for_microbial()
options = []
kingdoms = self.microbe_info.keys()
kingdoms.sort()
for kingdom in kingdoms:
options.append( (kingdom, kingdom, False) )
if options:
options[0] = ( options[0][0], options[0][1], True)
return options
def get_options_for_orgs_by_kingdom( self, trans, other_values ):
if self.microbe_info == None: self.load_from_file_for_microbial()
options = []
for func_param in self.func_params:
if func_param.get( 'name' ) == 'kingdom':
kingdom = other_values[ func_param.get( 'value' ) ]
orgs = self.microbe_info[kingdom].keys()
#need to sort by name
swap_test = False
for i in range( 0, len(orgs) - 1 ):
for j in range( 0, len(orgs) - i - 1 ):
if self.microbe_info[kingdom][orgs[j]]['name'] > self.microbe_info[kingdom][orgs[j + 1]]['name']:
orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j]
swap_test = True
if swap_test == False: break
for org in orgs:
if self.microbe_info[kingdom][org]['link_site'] == "UCSC":
options.append( ( "<b>" + self.microbe_info[kingdom][org]['name'] + "</b> <a href=\"" + self.microbe_info[kingdom][org]['info_url'] + "\" target=\"_blank\">(about)</a>", org, False ) )
else:
options.append( ( self.microbe_info[kingdom][org]['name'] + " <a href=\"" + self.microbe_info[kingdom][org]['info_url'] + "\" target=\"_blank\">(about)</a>", org, False ) )
if options:
options[0] = ( options[0][0], options[0][1], True)
return options
def get_options_for_kingdom_org_feature( self, trans, other_values ):
if self.microbe_info == None: self.load_from_file_for_microbial()
options = []
for func_param in self.func_params:
if func_param.get( 'name' ) == 'kingdom':
kingdom = other_values[ func_param.get( 'value' ) ]
elif func_param.get( 'name' ) == 'org':
org = other_values[ func_param.get( 'value' ) ]
elif func_param.get( 'name' ) == 'feature':
feature = func_param.get( 'value' )
log.debug("kingdom: %s, org: %s, feature: %s" %(kingdom, org, feature))
chroms = self.microbe_info[kingdom][org]['chrs'].keys()
chroms.sort()
for chr in chroms:
for data in self.microbe_info[kingdom][org]['chrs'][chr]['data']:
if self.microbe_info[kingdom][org]['chrs'][chr]['data'][data]['feature'] == feature:
options.append( ( self.microbe_info[kingdom][org]['chrs'][chr]['name'] + " <a href=\"" + self.microbe_info[kingdom][org]['chrs'][chr]['info_url'] + "\" target=\"_blank\">(about)</a>", data, False ) )
return options
lib/galaxy/tools/parameters.py
+2 -16
View File
@@ -407,29 +407,22 @@ class SelectToolParameter( ToolParameter ):
self.separator = elem.get( 'separator', ',' )
self.legal_values = set()
self.dynamic_options = elem.get( "dynamic_options", None )
select_options = elem.find( 'select_options' )
if select_options is None:
self.select_options = None
else:
self.select_options = dynamic_options.DynamicOptions( select_options )
options = elem.find( 'options' )
if options is None:
self.options = None
else:
self.options = dynamic_options.DynamicOptions( options )
if self.dynamic_options is None and self.select_options is None and self.options is None:
if self.dynamic_options is None and self.options is None:
self.static_options = list()
for index, option in enumerate( elem.findall( "option" ) ):
value = option.get( "value" )
self.legal_values.add( value )
selected = ( option.get( "selected", None ) == "true" )
self.static_options.append( ( option.text, value, selected ) )
self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.select_options is not None ) or ( self.options is not None ) )
self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) )
def get_options( self, trans, other_values ):
if self.options:
return self.options.get_options( trans, other_values )
elif self.select_options:
return eval( '''self.select_options.%s( trans, other_values )''' %self.select_options.func )
elif self.dynamic_options:
return eval( self.dynamic_options, self.tool.code_namespace, other_values )
else:
@@ -437,8 +430,6 @@ class SelectToolParameter( ToolParameter ):
def get_legal_values( self, trans, other_values ):
if self.options:
return set( v for _, v, _ in self.options.get_options( trans, other_values, must_be_valid = True ) )
elif self.select_options:
return set( v for _, v, _ in eval( '''self.select_options.%s( trans, other_values )''' %self.select_options.func ) )
elif self.dynamic_options:
return set( v for _, v, _ in eval( self.dynamic_options, self.tool.code_namespace, other_values ) )
else:
@@ -519,11 +510,6 @@ class SelectToolParameter( ToolParameter ):
except: pass
try: param_ref = self.options.param_ref
except: pass
elif self.select_options:
try: data_ref = self.select_options.data_ref
except: pass
try: param_ref = self.select_options.param_ref
except: pass
if data_ref is None and param_ref is None: return []
elif data_ref is None: return [ param_ref ]
elif param_ref is None: return [ data_ref ]
tools/data_source/encode_import_all_latest_datasets.xml
+2 -2
View File
@@ -6,13 +6,13 @@
<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
</display>
<param name="hg17" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" >
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="ALD" />
<filter type="param" name="build" value="hg17" />
</options>
</param>
<param name="hg16" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="ALD" />
<filter type="param" name="build" value="hg16" />
</options>
tools/data_source/encode_import_chromatin_and_chromosomes.xml
+2 -2
View File
@@ -6,13 +6,13 @@
<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
</display>
<param name="hg17" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="CC" />
<filter type="param" name="build" value="hg17" />
</options>
</param>
<param name="hg16" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="CC" />
<filter type="param" name="build" value="hg16" />
</options>
tools/data_source/encode_import_gencode.xml
+2 -2
View File
@@ -6,13 +6,13 @@
<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
</display>
<param name="hg17" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="GENCODE" />
<filter type="param" name="build" value="hg17" />
</options>
</param>
<param name="hg16" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="GENCODE" />
<filter type="param" name="build" value="hg16" />
</options>
tools/data_source/encode_import_genes_and_transcripts.xml
+2 -2
View File
@@ -6,13 +6,13 @@
<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
</display>
<param name="hg17" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="GT" />
<filter type="param" name="build" value="hg17" />
</options>
</param>
<param name="hg16" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="GT" />
<filter type="param" name="build" value="hg16" />
</options>
tools/data_source/encode_import_multi-species_sequence_analysis.xml
+2 -2
View File
@@ -6,13 +6,13 @@
<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
</display>
<param name="hg17" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="MSA" />
<filter type="param" name="build" value="hg17" />
</options>
</param>
<param name="hg16" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="MSA" />
<filter type="param" name="build" value="hg16" />
</options>
tools/data_source/encode_import_transcription_regulation.xml
+2 -2
View File
@@ -6,13 +6,13 @@
<p><div class="toolFormTitle">hg16 (most recent datasets in bold)</div>$hg16</p>
</display>
<param name="hg17" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="TR" />
<filter type="param" name="build" value="hg17" />
</options>
</param>
<param name="hg16" type="select" display="checkboxes" multiple="true">
<options from_file="/depot/data2/galaxy/encode_datasets.loc">
<options from_file="/depot/data2/galaxy/encode_datasets.loc" tool_type="encode">
<filter type="param" name="encode_group" value="TR" />
<filter type="param" name="build" value="hg16" />
</options>
tools/data_source/microbial_import.xml
+39 -39
View File
@@ -6,7 +6,7 @@
<p><div class="toolFormTitle">Select the Desired Kingdom</div>$kingdom</p>
</display>
<param name="kingdom" type="select" display="radio">
<select_options func="get_options_for_kingdoms" />
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial" />
</param>
</page>
<page>
@@ -14,9 +14,9 @@
<p><div class="toolFormTitle">Select the Desired Organism</div>$org</p>
</display>
<param name="org" type="select" display="radio">
<select_options func="get_options_for_orgs_by_kingdom">
<func_param name="kingdom" value="kingdom" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
</options>
</param>
</page>
<page>
@@ -30,53 +30,53 @@
<p><div class="toolFormTitle">Select Desired Glimmer3 Annotations</div>$Glimmer3</p>
</display>
<param name="CDS" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="CDS" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="CDS" />
</options>
</param>
<param name="tRNA" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="tRNA" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="tRNA" />
</options>
</param>
<param name="rRNA" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="rRNA" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="rRNA" />
</options>
</param>
<param name="sequence" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="sequence" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="sequence" />
</options>
</param>
<param name="GeneMark" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="GeneMark" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="GeneMark" />
</options>
</param>
<param name="GeneMarkHMM" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="GeneMarkHMM" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="GeneMarkHMM" />
</options>
</param>
<param name="Glimmer3" type="select" display="checkboxes" multiple="True">
<select_options func="get_options_for_kingdom_org_feature">
<func_param name="kingdom" value="kingdom" />
<func_param name="org" value="org" />
<func_param name="feature" value="Glimmer3" />
</select_options>
<options from_file="/depot/data2/galaxy/microbes/microbial_data.loc" tool_type="microbial">
<filter type="param_value" name="kingdom" value="kingdom" />
<filter type="param_value" name="org" value="org" />
<filter type="param" name="feature" value="Glimmer3" />
</options>
</param>
</page>
</inputs>
tools/data_source/microbial_import_code.py
+80
View File
@@ -1,7 +1,86 @@
def load_microbial_data( sep='\t' ):
# FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
# set data.name in exec_after_process().
microbe_info= {}
orgs = {}
for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ):
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#' ):
fields = line.split( sep )
#read each line, if not enough fields, go to next line
try:
info_type = fields.pop(0)
if info_type.upper() == "ORG":
#ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521
org_num = fields.pop(0)
name = fields.pop(0)
kingdom = fields.pop(0)
group = fields.pop(0)
chromosomes = fields.pop(0)
info_url = fields.pop(0)
link_site = fields.pop(0)
if org_num not in orgs:
orgs[ org_num ] = {}
orgs[ org_num ][ 'chrs' ] = {}
orgs[ org_num ][ 'name' ] = name
orgs[ org_num ][ 'kingdom' ] = kingdom
orgs[ org_num ][ 'group' ] = group
orgs[ org_num ][ 'chromosomes' ] = chromosomes
orgs[ org_num ][ 'info_url' ] = info_url
orgs[ org_num ][ 'link_site' ] = link_site
elif info_type.upper() == "CHR":
#CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1
org_num = fields.pop(0)
chr_acc = fields.pop(0)
name = fields.pop(0)
length = fields.pop(0)
gi = fields.pop(0)
gb = fields.pop(0)
info_url = fields.pop(0)
chr = {}
chr[ 'name' ] = name
chr[ 'length' ] = length
chr[ 'gi' ] = gi
chr[ 'gb' ] = gb
chr[ 'info_url' ] = info_url
if org_num not in orgs:
orgs[ org_num ] = {}
orgs[ org_num ][ 'chrs' ] = {}
orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr
elif info_type.upper() == "DATA":
#DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed
uid = fields.pop(0)
org_num = fields.pop(0)
chr_acc = fields.pop(0)
feature = fields.pop(0)
filetype = fields.pop(0)
path = fields.pop(0)
data = {}
data[ 'filetype' ] = filetype
data[ 'path' ] = path
data[ 'feature' ] = feature
if org_num not in orgs:
orgs[ org_num ] = {}
orgs[ org_num ][ 'chrs' ] = {}
if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]:
orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {}
orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data
else: continue
except: continue
for org_num in orgs:
org = orgs[ org_num ]
if org[ 'kingdom' ] not in microbe_info:
microbe_info[ org[ 'kingdom' ] ] = {}
if org_num not in microbe_info[ org[ 'kingdom' ] ]:
microbe_info[ org[ 'kingdom' ] ][org_num] = org
return microbe_info
#post processing, set build for data and add additional data to history
from galaxy import datatypes, config, jobs
from shutil import copyfile
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
history = out_data.items()[0][1].history
if history == None:
@@ -15,6 +94,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
if not (kingdom or org):
print "Parameters are not available."
microbe_info = load_microbial_data()
new_stdout = ""
split_stdout = stdout.split("\n")
basic_name = ""
tools/data_source/upload.xml
+4 -3
View File
@@ -11,8 +11,10 @@
<param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand.">
<option value="Yes">Yes</option>
</param>
<param type="select" name="file_type" label="File Format" dynamic_options="get_formats()" help="Which format? See help below" />
<param label="Genome" name="dbkey" type="genomebuild" dynamic_options=""/>
<param name="file_type" type="select" label="File Format" help="Which format? See help below">
<options tool_type="upload" />
</param>
<param name="dbkey" type="genomebuild" label="Genome" />
</inputs>
<help>
**Auto-detect**
@@ -128,5 +130,4 @@ Any data in tab delimited format (tabular)
Any text file
</help>
<code file="upload_code.py"/>
</tool>
tools/data_source/upload_code.py
-13
View File
@@ -1,13 +0,0 @@
from galaxy.datatypes import registry
def get_formats():
datatypes_registry = registry.Registry()
options = []
formats = datatypes_registry.datatypes_by_extension.keys()
formats.sort()
options.append(('Auto-detect','auto',True))
for format in formats:
label = format.capitalize()
options.append((label,format,False))
return options
tools/extract/interval2maf_pairwise.xml
+16 -7
View File
@@ -2,16 +2,26 @@
<description>given a set of genomic intervals</description>
<command interpreter="python2.4">interval2maf_pairwise.py --dbkey=$dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1</command>
<inputs>
<page>
<param format="interval" name="input1" type="data" label="Interval File"/>
</page>
<page>
<param name="mafType" label="Choose MAF source" type="select" dynamic_options="get_available_data( input1.dbkey )"/>
</page>
<param name="input1" type="data" format="interval" label="Interval File"/>
<param name="mafType" type="select" label="Choose MAF source">
<options from_file="/depot/data2/galaxy/maf_pairwise.loc">
<filter type="data_meta" data_ref="input1" key="build" />
<filter type="column" name="build_col" value="2" />
<filter type="column" name="name_col" value="0" />
<filter type="column" name="value_col" value="1" />
</options>
</param>
</inputs>
<outputs>
<data format="maf" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="8.bed" dbkey="hg17" format="bed"/>
<param name="mafType" value="PAIRWISE_hg17_fr1"/>
<output name="out_file1" file="Interval2Maf_pairwise_out.maf"/>
</test>
</tests>
<help>
**What it does**
@@ -26,5 +36,4 @@ Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are t
.. image:: ../static/images/maf_icons/interval2maf.png
</help>
<code file="interval2maf_pairwise_code.py"/>
</tool>
tools/extract/interval2maf_pairwise_code.py
-46
View File
@@ -1,46 +0,0 @@
#build list of available data
import os, sys
maf_sets = {}
try:
for line in open( "/depot/data2/galaxy/maf_pairwise.loc" ):
if line[0:1] == "#" : continue
fields = line.split('\t')
#read each line, if not enough fields, go to next line
try:
maf_desc = fields[0]
maf_uid = fields[1]
builds = fields[2]
build_list =[]
split_builds = builds.split(",")
for build in split_builds:
this_build = build.split("=")[0]
build_list.append(this_build)
paths = fields[3].replace("\n","").replace("\r","")
maf_sets[maf_uid]={}
maf_sets[maf_uid]['description']=maf_desc
maf_sets[maf_uid]['builds']=build_list
except:
continue
except Exception, exc:
print >>sys.stdout, 'interval2maf_pairwise_code.py initialization error -> %s' % exc
#return available datasets for group and build, set None option as selected for hg16
def get_available_data( build ):
available_sets = []
for key in maf_sets:
if build in maf_sets[key]['builds']:
available_sets.append((maf_sets[key]['description'],key,False))
if len(available_sets) < 1:
available_sets.append(('No data available for this build','None',True))
return available_sets
def exec_before_job(app,inp_data, out_data, param_dict, tool):
for name, data in out_data.items():
try:
data.name = data.name + " [" + maf_sets[param_dict['mafType']]['description'] + "]"
except KeyError:
data.name = data.name + " [unknown MAF source specified]"
tools/extract/interval_maf_to_merged_fasta.xml
+1 -1
View File
@@ -23,7 +23,7 @@
</when>
<when value="cached">
<param name="maf_identifier" type="select" label="MAF Type">
<options from_file="/depot/data2/galaxy/maf_index.loc" >
<options from_file="/depot/data2/galaxy/maf_index.loc">
<filter type="data_meta" data_ref="input1" key="build" />
<filter type="column" name="build_col" value="2" />
<filter type="column" name="name_col" value="0" />
tools/filters/maf/maf_stats_code.py
+30 -5
View File
@@ -1,12 +1,37 @@
def exec_before_job(app, inp_data, out_data, param_dict, tool):
def load_maf_data( sep='\t' ):
# FIXME: this function is duplicated in the DynamicOptions class. It is used here only to
# set data.name in exec_before_job().
maf_sets = {}
if param_dict['maf_source_type']['maf_source'] == "cached":
for line in open( "/depot/data2/galaxy/maf_index.loc" ):
line = line.rstrip( '\r\n' )
if line and not line.startswith( '#' ):
fields = line.split( sep )
#read each line, if not enough fields, go to next line
try:
maf_desc = fields[0]
maf_uid = fields[1]
builds = fields[2]
build_list =[]
split_builds = builds.split( "," )
for build in split_builds:
this_build = build.split( "=" )[0]
build_list.append( this_build )
paths = fields[3]
maf_sets[ maf_uid ] = {}
maf_sets[ maf_uid ][ 'description' ] = maf_desc
maf_sets[ maf_uid ][ 'builds' ] = build_list
except:
continue
return maf_sets
def exec_before_job(app, inp_data, out_data, param_dict, tool):
maf_sets = load_maf_data()
if param_dict[ 'maf_source_type' ][ 'maf_source' ] == "cached":
for name, data in out_data.items():
try:
data.name = data.name + " [" + maf_sets[str(param_dict['maf_source_type']['mafType'])]['description'] + "]"
data.name = data.name + " [" + maf_sets[ str( param_dict[ 'maf_source_type' ][ 'mafType' ] ) ][ 'description' ] + "]"
except KeyError:
data.name = data.name + " [unknown MAF source specified]"
if param_dict['summary'].lower() == "true":
if param_dict[ 'summary' ].lower() == "true":
for name, data in out_data.items():
data.change_datatype('tabular')
data.change_datatype( 'tabular' )
tools/filters/maf/maf_thread_for_species.xml
+1 -2
View File
@@ -50,7 +50,6 @@ results in::
</help>
<!--<code file="maf_thread_for_species_code.py"/>-->
</help>
</tool>
tools/filters/maf/maf_thread_for_species_code.py
-38
View File
@@ -1,38 +0,0 @@
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
# No initialization required.
#return lists of species available, showing gapped and ungapped base counts
def get_available_species( input_filename ):
try:
rval = []
species={}
file_in = open(input_filename, 'r')
try:
maf_reader = maf.Reader( file_in )
for i, m in enumerate( maf_reader ):
l = m.components
for c in l:
spec,chrom = maf.src_split( c.src )
if not spec or not chrom:
spec = chrom = c.src
if spec not in species:
species[spec]={"bases":0,"nongaps":0}
species[spec]["bases"] = species[spec]["bases"] + c.size + c.text.count("-")
species[spec]["nongaps"] = species[spec]["nongaps"] + c.size
file_in.close()
except:
return [("There is a problem with your MAF file",'None',True)]
species_names = species.keys()
species_names.sort()
for spec in species_names:
display = "%s: %i nongap, %i total bases" % (spec, species[spec]["nongaps"], species[spec]["bases"] )
rval.append( ( display,spec,True) )
return rval
except:
return [("<B>You must wait for the MAF file to be created before you can merge MAF blocks by species.</B>",'None',True)]
tools/regVariation/windowSplitter.xml
+1 -1
View File
@@ -2,7 +2,7 @@
<description></description>
<command interpreter="python2.4">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol</command>
<inputs>
<!--<param label="Genome" name="dbkey" type="genomebuild" dynamic_options=""/>-->
<!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
<param format="interval" name="input" type="data" label="Select data"/>
<param name="size" size="10" type="integer" value="500" label="Window size"/>
<conditional name="wintype">