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Requires change to Galaxy config - fixed the way the File Format select list in the upload tool is dynamically generated, now retrieved from the upload_file_formats in app.registry.

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Fixed all references to 'qualityscore' file extensions to be 'qual', since that is the extension in the QualityScore class.
Added functional test to the fastq2fasta converter.
This commit is contained in:
Greg Von Kuster
2008-05-28 16:01:29 +00:00
parent 051dc9ca94
commit f7806342fc
9 changed files with 94 additions and 57 deletions
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lib/galaxy/datatypes/registry.py
+33 -10
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@@ -14,27 +14,50 @@ class Registry( object ):
self.datatypes_by_extension = {}
self.mimetypes_by_extension = {}
self.datatype_converters = odict()
self.upload_file_formats = []
self.sniff_order = []
for ext, kind in datatypes:
# Data types are defined in the config like this:
# #<file extension> = <data type class>,<mime type (optional)>,<display in upload select list (optional)>
try:
mime_type = None
fields = kind.split(",")
if len(fields)>1:
kind = fields[0].strip()
mime_type = fields[1].strip()
kind = fields[0].strip()
mime_type = None
display_in_upload = False
# See if we have a mime type or a display_in_upload
try:
ele = fields[1].strip()
if ele:
if ele == 'display_in_upload':
display_in_upload = True
else:
mime_type = ele
except:
pass
# See if we have a display_in_upload
if not display_in_upload:
try:
ele = fields[2].strip()
if ele == 'display_in_upload':
display_in_upload = True
except:
pass
if display_in_upload:
self.upload_file_formats.append( ext )
fields = kind.split(":")
datatype_module = fields[0]
datatype_class = fields[1]
fields = datatype_module.split(".")
module = __import__(fields.pop(0))
for mod in fields: module = getattr(module,mod)
module = __import__( fields.pop(0) )
for mod in fields:
module = getattr(module,mod)
self.datatypes_by_extension[ext] = getattr(module, datatype_class)()
if mime_type is None:
# Use default mime type as per datatype spec
mime_type = self.datatypes_by_extension[ext].get_mime()
self.mimetypes_by_extension[ext] = mime_type
except:
self.log.warning('error loading datatype: %s' % ext)
except Exception, e:
self.log.warning('error loading datatype "%s", problem: %s' % ( ext, str( e ) ) )
#default values
if len(self.datatypes_by_extension) < 1:
self.datatypes_by_extension = {
@@ -51,7 +74,7 @@ class Registry( object ):
'laj' : images.Laj(),
'lav' : sequence.Lav(),
'maf' : sequence.Maf(),
'qualityscore': qualityscore.QualityScore(),
'qual' : qualityscore.QualityScore(),
'scf' : images.Scf(),
'tabular' : tabular.Tabular(),
'taxonomy' : tabular.Taxonomy(),
@@ -73,7 +96,7 @@ class Registry( object ):
'laj' : 'text/plain',
'lav' : 'text/plain',
'maf' : 'text/plain',
'qualityscore': 'text/plain',
'qual' : 'text/plain',
'scf' : 'application/octet-stream',
'tabular' : 'text/plain',
'taxonomy' : 'text/plain',
lib/galaxy/tools/parameters/dynamic_options.py
+6 -7
View File
@@ -172,8 +172,8 @@ class DynamicOptions( object ):
filters[ 'data_meta' ][ 'meta_value' ] = dataset.metadata.species
except:
pass
return self.generate_options( filters=filters, sep=self.separator )
def generate_options( self, filters={}, sep='\t' ):
return self.generate_options( trans, filters=filters, sep=self.separator )
def generate_options( self, trans, filters={}, sep='\t' ):
try:
meta_key = filters[ 'data_meta' ][ 'meta_key' ]
except:
@@ -194,7 +194,8 @@ class DynamicOptions( object ):
return self.generate_for_dbkey( dbkey, meta_key_col, self.name_col, self.value_col, sep=sep )
else: # meta_key is None
if self.data_file == 'datatypes_registry':
return self.generate_from_datatypes_registry()
upload_file_formats = trans.app.datatypes_registry.upload_file_formats
return self.generate_from_datatypes_registry( upload_file_formats )
elif self.data_file == 'encode_datasets.loc':
encode_group = filters[ 'params' ][ 'encode_group' ]
dbkey = filters[ 'params' ][ 'dbkey' ]
@@ -217,11 +218,9 @@ class DynamicOptions( object ):
return self.generate_for_microbial( kingdom, org, feature )
else:
return self.generate( self.name_col, self.value_col, sep=sep )
def generate_from_datatypes_registry( self ):
from galaxy.datatypes import registry
datatypes_registry = registry.Registry()
def generate_from_datatypes_registry( self, upload_file_formats ):
options = []
formats = datatypes_registry.datatypes_by_extension.keys()
formats = upload_file_formats
formats.sort()
options.append( ( 'Auto-detect', 'auto', True ) )
for format in formats:
test-data/1.fastq
+8
View File
@@ -0,0 +1,8 @@
@seq1
GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
+seq1
hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
@seq2
GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
+seq2
hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
tools/metag_tools/convert_fastq2fasta.xml
+17 -11
View File
@@ -1,15 +1,21 @@
<tool id="convert_fastq2fasta" name="FASTQ-to-FASTA" version="1.0.0">
<description>converts FASTQ file to FASTA format</description>
<command interpreter="python">convert_fastq2fasta.py $input1 $output1 $output2</command>
<inputs>
<param name="input1" type="data" format="fastq" label="Fastq file"/>
</inputs>
<outputs>
<data name="output1" format="fasta"/>
<data name="output2" format="qualityscore"/>
</outputs>
<help>
<description>converts FASTQ file to FASTA format</description>
<command interpreter="python">convert_fastq2fasta.py $input1 $output1 $output2</command>
<inputs>
<param name="input1" type="data" format="fastq" label="Fastq file"/>
</inputs>
<outputs>
<data name="output1" format="qual"/>
<data name="output2" format="fasta"/>
</outputs>
<tests>
<!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
<test>
<param name="input1" value="1.fastq" ftype="fastq" />
<output name="output2" file="convert_fastq2fasta_out2.fasta" />
</test>
</tests>
<help>
**What it does**
tools/metag_tools/rmapq_wrapper.xml
+2 -2
View File
@@ -10,7 +10,7 @@
<options from_file="faseq.loc" name_col="0" value_col="1"/>
</param>
<param name="input_seq" type="data" format="fasta" label="Sequence file"/>
<param name="input_score" type="data" format="qualityscore" label="Quality score file"/>
<param name="input_score" type="data" format="qual" label="Quality score file"/>
<param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
<param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
<param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
@@ -43,7 +43,7 @@
<test>
<param name="database" value="/depot/data2/galaxy/faseq/test" />
<param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
<param name="input_score" value="rmapq_wrapper_test1.qualityscore" ftype="qualityscore" />
<param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qual" />
<param name="high_score" value="40" />
<param name="high_len" value="36" />
<param name="read_len" value="36" />
tools/metag_tools/short_reads_figure_high_quality_length.xml
+3 -3
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@@ -5,7 +5,7 @@
<inputs>
<page>
<param name="input1" type="data" format="qualityscore,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
<param name="input1" type="data" format="qual,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
<param name="input2" type="integer" size="5" value="20" label="Quality score threshold" />
</page>
</inputs>
@@ -17,12 +17,12 @@
</requirements>
<tests>
<test>
<param name="input1" value="solexa.qualityscore" ftype="qualityscore" />
<param name="input1" value="solexa.qual" ftype="qual" />
<param name="input2" value="5" />
<output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/>
</test>
<test>
<param name="input1" value="454.qualityscore" ftype="qualityscore" />
<param name="input1" value="454.qual" ftype="qual" />
<param name="input2" value="5" />
<output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/>
</test>
tools/metag_tools/short_reads_figure_score.xml
+3 -3
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@@ -5,7 +5,7 @@
<inputs>
<page>
<param name="input1" type="data" format="qualityscore, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
<param name="input1" type="data" format="qual, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
</page>
</inputs>
@@ -17,11 +17,11 @@
</requirements>
<tests>
<test>
<param name="input1" value="solexa.qualityscore" ftype="qualityscore" />
<param name="input1" value="solexa.qual" ftype="qual" />
<output name="output1" file="solexaScore.png" ftype="png" />
</test>
<test>
<param name="input1" value="454.qualityscore" ftype="qualityscore" />
<param name="input1" value="454.qual" ftype="qual" />
<output name="output1" file="454Score.png" ftype="png" />
</test>
</tests>
tools/metag_tools/short_reads_trim_seq.xml
+3 -3
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@@ -7,7 +7,7 @@
<inputs>
<page>
<param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" />
<param name="input2" type="data" format="qualityscore,txtseq.zip" label="Quality scores" />
<param name="input2" type="data" format="qual,txtseq.zip" label="Quality scores" />
<param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
<param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
<conditional name="sequencing_method_choice">
@@ -36,7 +36,7 @@
<test>
<param name="sequencer" value="454" />
<param name="input1" value="454.fasta" ftype="fasta" />
<param name="input2" value="454.qualityscore" ftype="qualityscore" />
<param name="input2" value="454.qual" ftype="qual" />
<param name="input3" value="no" />
<param name="trim" value="20" />
<param name="length" value="0" />
@@ -45,7 +45,7 @@
<test>
<param name="sequencer" value="Solexa" />
<param name="input1" value="solexa.fasta" ftype="fasta" />
<param name="input2" value="solexa.qualityscore" ftype="qualityscore" />
<param name="input2" value="solexa.qual" ftype="qual" />
<param name="input3" value="0" />
<param name="trim" value="20" />
<param name="length" value="0" />
universe_wsgi.ini.sample
+19 -18
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@@ -85,7 +85,7 @@ mailing_join_addr = galaxy-user-join@bx.psu.edu
# Mail
smtp_server = coltrane.bx.psu.edu
error_email_to = galaxy_bugs@bx.psu.edu
error_email_to = galaxy-bugs@bx.psu.edu
# Use the new iframe / javascript based layout
use_new_layout = true
@@ -167,33 +167,34 @@ upload1 = local:///
[galaxy:datatypes]
ab1 = galaxy.datatypes.images:Ab1,application/octet-stream
axt = galaxy.datatypes.sequence:Axt
bed = galaxy.datatypes.interval:Bed
binseq.zip = galaxy.datatypes.images:Binseq,application/zip
#<file extension> = <data type class>,<mime type (optional)>,<display in upload select list (optional)>
ab1 = galaxy.datatypes.images:Ab1,application/octet-stream,display_in_upload
axt = galaxy.datatypes.sequence:Axt,display_in_upload
bed = galaxy.datatypes.interval:Bed,display_in_upload
binseq.zip = galaxy.datatypes.images:Binseq,application/zip,display_in_upload
customtrack = galaxy.datatypes.interval:CustomTrack
data = galaxy.datatypes.data:Data,application/octet-stream
fasta = galaxy.datatypes.sequence:Fasta
fastq = galaxy.datatypes.sequence:Fastq
gff = galaxy.datatypes.interval:Gff
gff3 = galaxy.datatypes.interval:Gff3
fasta = galaxy.datatypes.sequence:Fasta,display_in_upload
fastq = galaxy.datatypes.sequence:Fastq,display_in_upload
gff = galaxy.datatypes.interval:Gff,display_in_upload
gff3 = galaxy.datatypes.interval:Gff3,display_in_upload
gif = galaxy.datatypes.images:Image,image/gif
gmaj.zip = galaxy.datatypes.images:Gmaj,application/zip
html = galaxy.datatypes.images:Html,text/html
interval = galaxy.datatypes.interval:Interval
interval = galaxy.datatypes.interval:Interval,display_in_upload
jpg = galaxy.datatypes.images:Image,image/jpeg
laj = galaxy.datatypes.images:Laj
lav = galaxy.datatypes.sequence:Lav
maf = galaxy.datatypes.sequence:Maf
maf = galaxy.datatypes.sequence:Maf,display_in_upload
pdf = galaxy.datatypes.images:Image,application/pdf
png = galaxy.datatypes.images:Image,image/png
qualityscore = galaxy.datatypes.qualityscore:QualityScore
scf = galaxy.datatypes.images:Scf,application/octet-stream
taxonomy = galaxy.datatypes.tabular:Taxonomy
tabular = galaxy.datatypes.tabular:Tabular
txt = galaxy.datatypes.data:Text
txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip
wig = galaxy.datatypes.interval:Wiggle
qual = galaxy.datatypes.qualityscore:QualityScore,display_in_upload
scf = galaxy.datatypes.images:Scf,application/octet-stream,display_in_upload
taxonomy = galaxy.datatypes.tabular:Taxonomy,display_in_upload
tabular = galaxy.datatypes.tabular:Tabular,display_in_upload
txt = galaxy.datatypes.data:Text,display_in_upload
txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip,display_in_upload
wig = galaxy.datatypes.interval:Wiggle,display_in_upload
#EMBOSS TOOLS
acedb = galaxy.datatypes.data:Text
asn1 = galaxy.datatypes.data:Text