mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Initial GeneTrack commit. Most parts are in, but dependencies will still be a problem.
This commit is contained in:
Ian Schenck
@@ -82,6 +82,8 @@
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<datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
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<datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
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<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/>
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<datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage"/>
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<datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
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<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
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@@ -0,0 +1,30 @@
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"""
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Coverage datatypes
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"""
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import logging, os, sys, time, sets, tempfile, shutil
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import data
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from galaxy import util
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from galaxy.datatypes.sniff import *
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from galaxy.web import url_for
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from cgi import escape
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import urllib
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from bx.intervals.io import *
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from galaxy.datatypes import metadata
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from galaxy.datatypes.metadata import MetadataElement
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from galaxy.datatypes.tabular import Tabular
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log = logging.getLogger(__name__)
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class LastzCoverage( Tabular ):
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file_ext = "coverage"
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MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
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MetadataElement( name="positionCol", default=2, desc="Position column", param=metadata.ColumnParameter )
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MetadataElement( name="forwardCol", default=3, desc="Forward or aggregate read column", param=metadata.ColumnParameter )
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MetadataElement( name="reverseCol", desc="Optional reverse read column", param=metadata.ColumnParameter, optional=True, no_value=0 )
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MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )
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@@ -3,7 +3,7 @@ Provides mapping between extensions and datatypes, mime-types, etc.
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"""
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import os
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import logging
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import data, tabular, interval, images, sequence, qualityscore, genetics, xml
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import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks
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import galaxy.util
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from galaxy.util.odict import odict
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@@ -97,12 +97,14 @@ class Registry( object ):
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'bed' : interval.Bed(),
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'binseq.zip' : images.Binseq(),
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'blastxml' : xml.BlastXml(),
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'coverage' : coverage.LastzCoverage(),
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'customtrack' : interval.CustomTrack(),
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'csfasta' : sequence.csFasta(),
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'fasta' : sequence.Fasta(),
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'fastqsolexa' : sequence.FastqSolexa(),
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'gff' : interval.Gff(),
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'gff3' : interval.Gff3(),
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'gff3' : interval.Gff3(),
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'genetrack' : tracks.GeneTrack(),
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'interval' : interval.Interval(),
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'laj' : images.Laj(),
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'lav' : sequence.Lav(),
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@@ -0,0 +1,30 @@
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"""
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Datatype classes for tracks/track views within galaxy.
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"""
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import data
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import logging
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import re
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from cgi import escape
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from galaxy.datatypes.metadata import MetadataElement
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from galaxy.datatypes import metadata
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import galaxy.model
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from galaxy import util
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from galaxy.web import url_for
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from sniff import *
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log = logging.getLogger(__name__)
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class GeneTrack( data.Binary ):
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file_ext = "genetrack"
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MetadataElement( name="hdf", default="data.hdf", desc="HDF DB", readonly=True, visible=True, no_value=0 )
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MetadataElement( name="sqlite", default="features.sqlite", desc="SQLite Features DB", readonly=True, visible=True, no_value=0 )
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MetadataElement( name="label", default="Custom", desc="Track Label", readonly=True, visible=True, no_value="Custom" )
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def __init__(self, **kwargs):
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super(GeneTrack, self).__init__(**kwargs)
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self.add_display_app( 'genetrack', 'View in ', '', 'genetrack_link' )
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def genetrack_link( self, dataset, type, app, base_url ):
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return [('GeneTrack', url_for(controller='genetrack', action='index', dataset_id=dataset.id ))]
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@@ -0,0 +1,161 @@
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import time, glob, os
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import pkg_resources
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pkg_resources.require("GeneTrack")
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import atlas
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from atlas import sql
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from atlas import util as atlas_utils
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from atlas.web import formlib
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from mako import exceptions
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from mako.template import Template
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from mako.lookup import TemplateLookup
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from galaxy.web.base.controller import *
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pkg_resources.require( "Paste" )
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import paste.httpexceptions
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# SETUP Track Builders
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from mod454.trackbuilder import build_tracks
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import functools
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def twostrand_tracks( param=None, conf=None ):
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return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='twostrand')
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def composite_tracks( param=None, conf=None ):
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return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='composite')
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class BaseConf( object ):
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"""
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Fake web_conf for atlas.
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"""
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IMAGE_DIR = "static/genetrack/plots/"
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LEVELS = [str(x) for x in [ 50, 100, 250, 500, 1000, 2500, 5000, 10000, 20000, 50000, 100000, 200000 ]]
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ZOOM_LEVELS = zip(LEVELS, LEVELS)
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PLOT_SETUP = [
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('comp-id', 'Composite' , 'genetrack/index.html', composite_tracks ),
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('two-id' , 'Two Strand', 'genetrack/index.html', twostrand_tracks ),
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]
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PLOT_CHOICES = [ (id, name) for (id, name, page, func) in PLOT_SETUP ]
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PLOT_MAPPER = dict( [ (id, (page, func)) for (id, name, page, func) in PLOT_SETUP ] )
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def __init__(self, **kwds):
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for key,value in kwds.items():
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setattr( self, key, value)
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class WebRoot(BaseController):
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@web.expose
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def search(self, trans, word='', dataset_id=None, submit=''):
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"""
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Default search page
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"""
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data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
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if not data:
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raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
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# the main configuration file
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conf = BaseConf(
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TITLE = "<i>%s</i>: %s" % (data.metadata.dbkey, data.metadata.label),
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HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ),
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SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ),
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LABEL = data.metadata.label,
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FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
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PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
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)
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from atlas import hdf
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db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
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conf.CHROM_FIELDS = [(x,x) for x in hdf.GroupData(db=db, name=conf.LABEL).labels]
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db.close()
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param = atlas.Param( word=word )
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# search with features based on param.feature
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# search for a given
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session = sql.get_session( conf.SQL_URI )
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if param.word:
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def search_query( word, text ):
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query = session.query(sql.Feature).filter( "name LIKE :word or freetext LIKE :text" ).params(word=word, text=text)
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query = list(query[:20])
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return query
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# a little heuristics to match most likely target
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targets = [
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(param.word+'%', 'No match'), # match beginning
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('%'+param.word+'%', 'No match'), # match name anywhere
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('%'+param.word+'%', '%'+param.word+'%'), # match json anywhere
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]
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for word, text in targets:
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query = search_query( word=word, text=text)
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if query:
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break
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else:
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query = []
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return trans.fill_template_mako('genetrack/search.html', param=param, query=query, dataset_id=dataset_id)
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@web.expose
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def index(self, trans, dataset_id=None, **kwds):
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"""
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Main request handler
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"""
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data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
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if not data:
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raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
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# the main configuration file
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conf = BaseConf(
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TITLE = "<i>%s</i>: %s" % (data.metadata.dbkey, data.metadata.label),
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HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ),
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SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ),
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LABEL = data.metadata.label,
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FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
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PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
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)
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from atlas import hdf
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db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
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conf.CHROM_FIELDS = [(x,x) for x in hdf.GroupData(db=db, name=conf.LABEL).labels]
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db.close()
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# generate a new form based on the configuration
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form = formlib.main_form( conf )
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# clear the tempdir every once in a while
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atlas_utils.clear_tempdir( dir=conf.IMAGE_DIR, days=1, chance=10)
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incoming = form.defaults()
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incoming.update( kwds )
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# manage the zoom and pan requests
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incoming = formlib.zoom_change( kdict=incoming, levels=conf.LEVELS)
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incoming = formlib.pan_view( kdict=incoming )
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# process the form
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param = atlas.Param( **incoming )
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form.process( incoming )
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if kwds and form.isSuccessful():
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# adds the sucessfull parameters
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param.update( form.values() )
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# if it was a search word not a number go to search page
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try:
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center = int( param.feature )
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except ValueError:
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# go and search for these
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return trans.response.send_redirect( web.url_for( controller='genetrack', action='search', word=param.feature, dataset_id=dataset_id ) )
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# keep image at a sane size
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param.width = min( [2000, int(param.img_size)] )
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# get the template and the function used to generate the tracks
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tmpl_name, track_maker = conf.PLOT_MAPPER[param.plot]
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if track_maker is not None:
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# generate the name that the image will be stored at
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fname, fpath = atlas_utils.make_tempfile( dir=conf.IMAGE_DIR, suffix='.png')
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param.fname = fname
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# generate the track
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track_chart = track_maker( param=param, conf=conf )
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track_chart.save(fname=fpath)
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return trans.fill_template_mako(tmpl_name, conf=conf, form=form, param=param, dataset_id=dataset_id)
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+1
-1
@@ -12,7 +12,7 @@ assert sys.version_info[:2] >= ( 2, 4 )
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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print sys.path
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from galaxy import eggs
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import pkg_resources
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@@ -0,0 +1,78 @@
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body {
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font-family: "Trebuchet MS", Arial, tahoma, sans-serif;
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font-size: 14px;
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line-height: 1.6em;
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margin: 0;
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padding: 0;
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border-top: 9px solid #CCD9FF;
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}
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/* Error message style */
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.error{
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background: #FFFF66;
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}
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/* Error message style */
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.message{
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background: #33FF66;
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}
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/* Odd data row in the table */
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.selected {
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background-color: #FFFFCC;
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}
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.nav_button{
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background-color:#EEEEEE;
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border:1px solid;
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color: #000000;
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}
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.nav_button:hover{
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background-color:#000000;
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border:1px solid;
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color: #FFFFFF;
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}
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.grey {
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background-color: #EFEFEF;
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}
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.odd {
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background-color: #ECECEC;
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}
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.even {
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background-color: #FFFFFF;
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}
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|
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/* Text table style */
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.data_table {
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border: 1px solid #CCCCCC;
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background-color: white;
|
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}
|
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|
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/* Footer is added to every page */
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#footer {
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background: #EFEFEF;
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text-align:center;
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padding:.2em;
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border-top: 1px solid #CCD9FF;
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border-bottom: 1px solid #CCD9FF;
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clear: both;
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}
|
||||
|
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#footer p {
|
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font-size:.94em; line-height:2em; color:#cccccc; margin: 0;
|
||||
}
|
||||
|
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#tag {
|
||||
font-size:.80em; margin: 4px; padding: 2px;
|
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}
|
||||
|
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|
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#footer img {
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vertical-align: middle; margin-left: 3px; padding-bottom: 2px;
|
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}
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|
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@@ -0,0 +1,79 @@
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var cookie_name = "genetrack_ui"
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var now = new Date();
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now.setTime(now.getTime() + 365 * 24 * 60 * 60 * 1000);
|
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|
||||
// this toggles between none and block
|
||||
function toggle(name){
|
||||
var elem = get(name)
|
||||
if (elem) {
|
||||
if (elem.style.display=="none"){
|
||||
elem.style.display="block"
|
||||
setCookie(cookie_name, name, now)
|
||||
} else {
|
||||
elem.style.display="none"
|
||||
setCookie(cookie_name, '', now)
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
function main(){
|
||||
//executed upon main body load
|
||||
var value = getCookie(cookie_name);
|
||||
toggle( value )
|
||||
}
|
||||
|
||||
// this toggles between visible and hidden
|
||||
function show(name){
|
||||
var elem = get(name)
|
||||
if (elem.style.visibility=="hidden"){
|
||||
elem.style.visibility="visible";
|
||||
} else {
|
||||
elem.style.visibility="hidden";
|
||||
}
|
||||
}
|
||||
|
||||
// utility function to get the length of on object
|
||||
function len(obj){
|
||||
return obj.length;
|
||||
}
|
||||
|
||||
// utility function to get an element by id
|
||||
function get(name){
|
||||
return document.getElementById(name);
|
||||
}
|
||||
|
||||
// pops up a window
|
||||
function pop_up(url) {
|
||||
day = new Date();
|
||||
id = day.getTime();
|
||||
eval("page" + id + " = window.open(url, '" + id + "', 'toolbar=0,scrollbars=1,location=0,statusbar=1,menubar=0,resizable=1,width=500,height=300');");
|
||||
}
|
||||
|
||||
//
|
||||
// cookie management off the web
|
||||
// http://www.webreference.com/js/column8/property.html
|
||||
//
|
||||
function setCookie(name, value, expires, path, domain, secure) {
|
||||
var curCookie = name + "=" + escape(value) +
|
||||
((expires) ? "; expires=" + expires.toGMTString() : "") +
|
||||
((path) ? "; path=" + path : "") +
|
||||
((domain) ? "; domain=" + domain : "") +
|
||||
((secure) ? "; secure" : "");
|
||||
document.cookie = curCookie;
|
||||
}
|
||||
|
||||
function getCookie(name) {
|
||||
var dc = document.cookie;
|
||||
var prefix = name + "=";
|
||||
var begin = dc.indexOf("; " + prefix);
|
||||
if (begin == -1) {
|
||||
begin = dc.indexOf(prefix);
|
||||
if (begin != 0) return null;
|
||||
} else
|
||||
begin += 2;
|
||||
var end = document.cookie.indexOf(";", begin);
|
||||
if (end == -1)
|
||||
end = dc.length;
|
||||
return unescape(dc.substring(begin + prefix.length, end));
|
||||
}
|
||||
@@ -11,7 +11,6 @@
|
||||
<tool file="data_source/wormbase.xml" />
|
||||
<tool file="data_source/wormbase_test.xml" />
|
||||
<tool file="data_source/flymine.xml" />
|
||||
<tool file="data_source/flymine_test.xml" />
|
||||
<tool file="data_source/encode_db.xml" />
|
||||
<tool file="data_source/epigraph_import.xml" />
|
||||
<tool file="data_source/epigraph_import_test.xml" />
|
||||
@@ -302,4 +301,7 @@
|
||||
<tool file="metag_tools/blat_wrapper.xml" />
|
||||
<tool file="metag_tools/mapping_to_ucsc.xml" />
|
||||
</section>
|
||||
<section name="Tracks" id="tracks">
|
||||
<tool file="visualization/genetrack.xml" />
|
||||
</section>
|
||||
</toolbox>
|
||||
|
||||
@@ -82,7 +82,7 @@
|
||||
<when input="out_format" value="maf" format="maf" />
|
||||
</change_format>
|
||||
</data>
|
||||
<data format="tabular" name="output2" />
|
||||
<data format="coverage" name="output2" />
|
||||
</outputs>
|
||||
<requirements>
|
||||
<requirement type="binary">lastz</requirement>
|
||||
|
||||
@@ -0,0 +1,139 @@
|
||||
#!/usr/bin/env python
|
||||
"""
|
||||
Run GeneTrack(atlas) with a faked conf file to generate GeneTrack data files.
|
||||
|
||||
usage: %prog
|
||||
-l, --label=N: Data label for fit curve/peak plot
|
||||
-1, --fits=N/N/N/N/N,...: Data files (interval format) for fit curve/peak plot
|
||||
-2, --feats=N:M/N/N/N/N/N,...: Data files (interval format) for features.
|
||||
-d, --data=N: Output path for hdf5 and sqlite databases.
|
||||
-o, --output=N: Output path for export file.
|
||||
"""
|
||||
from galaxy import eggs
|
||||
import pkg_resources
|
||||
pkg_resources.require("GeneTrack")
|
||||
pkg_resources.require("bx-python")
|
||||
|
||||
from atlas import commands
|
||||
from bx.cookbook import doc_optparse
|
||||
import os
|
||||
import commands as oscommands
|
||||
import tempfile
|
||||
|
||||
SIGMA = 20
|
||||
WIDTH = 5 * SIGMA
|
||||
EXCLUSION_ZONE = 147
|
||||
|
||||
def main(label, fit, feats, data_dir, output):
|
||||
os.mkdir(data_dir)
|
||||
conf = DummyConf(
|
||||
__name__=label,
|
||||
CLOBBER = True,
|
||||
DATA_SIZE = 3*10**6,
|
||||
MINIMUM_PEAK_SIZE = 0.1,
|
||||
LOADER_ENABLED = True,
|
||||
FITTER_ENABLED = True,
|
||||
PREDICTOR_ENABLED = True,
|
||||
EXPORTER_ENABLED = True,
|
||||
LOADER = loader,
|
||||
FITTER = fitter,
|
||||
PREDICTOR = predictor,
|
||||
EXPORTER = exporter,
|
||||
HDF_DATABASE = os.path.join( data_dir, "data.hdf" ),
|
||||
SQL_URI = "sqlite:///%s" % os.path.join( data_dir, "features.sqlite" ),
|
||||
SIGMA = SIGMA,
|
||||
WIDTH = WIDTH,
|
||||
DATA_LABEL = label,
|
||||
FIT_LABEL = "%s-SIGMA-%d" % ( label,SIGMA ),
|
||||
PEAK_LABEL = "PRED-%s-SIGMA-%d" % ( label,SIGMA ),
|
||||
EXCLUSION_ZONE = EXCLUSION_ZONE,
|
||||
LEFT_SHIFT = EXCLUSION_ZONE / 2,
|
||||
RIGHT_SHIFT = EXCLUSION_ZONE / 2,
|
||||
EXPORT_LABELS = [ "PRED-%s-SIGMA-%d" % ( label,SIGMA ) ],
|
||||
EXPORT_DIR = os.path.join( data_dir ),
|
||||
DATA_FILE=fit[1],
|
||||
fit=fit,
|
||||
feats=feats,
|
||||
)
|
||||
commands.execute(conf)
|
||||
|
||||
# mod454 seems to be a module without a package. The necessary funcitons are
|
||||
# stubbed out here until I'm sure of their final home. INS
|
||||
|
||||
def loader( conf ):
|
||||
from atlas import hdf
|
||||
from mod454.schema import Mod454Schema as Schema
|
||||
last_chrom = table = None
|
||||
db = hdf.hdf_open( conf.HDF_DATABASE, mode='a', title='HDF database')
|
||||
gp = hdf.create_group( db=db, name=conf.DATA_LABEL, desc='data group', clobber=conf.CLOBBER )
|
||||
fit_meta = conf.fit[2]
|
||||
# iterate over the file and insert into table
|
||||
for line in open( conf.fit[1], "r" ):
|
||||
if line.startswith("chrom"): continue #Skip possible header
|
||||
if line.startswith("#"): continue
|
||||
fields = line.rstrip('\r\n').split('\t')
|
||||
chrom = fields[fit_meta.chromCol]
|
||||
if chrom != last_chrom:
|
||||
if table: table.flush()
|
||||
table = hdf.create_table( db=db, name=chrom, where=gp, schema=Schema, clobber=False )
|
||||
last_chrom = chrom
|
||||
try:
|
||||
position = int(fields[fit_meta.positionCol])
|
||||
forward = float(fields[fit_meta.forwardCol])
|
||||
reverse = fit_meta.reverseCol > -1 and float(fields[fit_meta.reverseCol]) or 0.0
|
||||
row = ( position, forward, reverse, forward+reverse, )
|
||||
table.append( [ row ] )
|
||||
except ValueError:
|
||||
# Ignore bad lines
|
||||
pass
|
||||
table.flush()
|
||||
db.close()
|
||||
|
||||
def fitter( conf ):
|
||||
from mod454.fitter import fitter as mod454_fitter
|
||||
return mod454_fitter( conf )
|
||||
|
||||
def predictor( conf ):
|
||||
from mod454.predictor import predictor as mod454_predictor
|
||||
return mod454_predictor( conf )
|
||||
|
||||
def exporter( conf ):
|
||||
return commands.bed_exporter(conf)
|
||||
|
||||
class Bunch( object ):
|
||||
def __init__(self, **kwargs):
|
||||
for key,value in kwargs.items():
|
||||
setattr( self, key, value )
|
||||
|
||||
class DummyConf( Bunch ):
|
||||
"""
|
||||
Fake conf module for genetrack/atlas.
|
||||
"""
|
||||
pass
|
||||
|
||||
if __name__ == "__main__":
|
||||
options, args = doc_optparse.parse( __doc__ )
|
||||
try:
|
||||
label = options.label
|
||||
fit_name, fit_meta = options.fits.split(':')[0], [int(x)-1 for x in options.fits.split(':')[1:]]
|
||||
fit_meta = Bunch(chromCol=fit_meta[0], positionCol=fit_meta[1], forwardCol=fit_meta[2], reverseCol=fit_meta[3])
|
||||
fit = ( label, fit_name, fit_meta, )
|
||||
# split apart the string into nested lists, preserves order
|
||||
if options.feats:
|
||||
feats = [ (
|
||||
feat_label,
|
||||
fname,
|
||||
Bunch(chromCol=int(chromCol)-1, startCol=int(startCol)-1, endCol=int(endCol)-1,
|
||||
strandCol=int(strandCol)-1, nameCol=int(nameCol)-1),
|
||||
)
|
||||
for feat_label, fname, chromCol, startCol, endCol, strandCol, nameCol
|
||||
in ( feat.split(':') for feat in options.feats.split(',') )]
|
||||
else:
|
||||
feats = []
|
||||
data_dir = options.data
|
||||
output = options.output
|
||||
except:
|
||||
doc_optparse.exception()
|
||||
|
||||
main(label, fit, feats, data_dir, output)
|
||||
|
||||
@@ -0,0 +1,53 @@
|
||||
<tool id="genetrack1" name="GeneTrack">
|
||||
|
||||
<description>Track creator/viewer</description>
|
||||
|
||||
<code file="genetrack_code.py">
|
||||
<hook exec_after_process="exec_after_process" />
|
||||
</code>
|
||||
|
||||
<command interpreter="python">
|
||||
genetrack.py -l $data_label
|
||||
-1 ${fit_data}:${fit_data.metadata.chromCol}:${fit_data.metadata.positionCol}:${fit_data.metadata.forwardCol}:${fit_data.metadata.reverseCol}
|
||||
#if $feature_data
|
||||
-2
|
||||
#end if
|
||||
#for $data in $feature_data
|
||||
${data.name}:${data.input}:${data.input.metadata.chromCol}:${data.input.metadata.startCol}:${data.input.metadata.endCol}:${data.input.metadata.strandCol}:${data.input.metadata.nameCol},
|
||||
#end for
|
||||
-d ${genetrack.files_path}
|
||||
-o ${bed_out}
|
||||
</command>
|
||||
|
||||
<inputs>
|
||||
<param name="data_label" type="text" label="Track Label" size="50">
|
||||
<validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{0,25}</validator>
|
||||
</param>
|
||||
<param name="fit_data" type="data" format="coverage" label="Coverage Dataset" />
|
||||
<repeat name="feature_data" title="Features">
|
||||
<param name="input" type="data" format="interval" label="Dataset" />
|
||||
<param name="name" type="text" label="Feature Type (mRNA, ESTs, ORFs, etc.)" size="25">
|
||||
<validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{0,25}</validator>
|
||||
</param>
|
||||
</repeat>
|
||||
</inputs>
|
||||
|
||||
<outputs>
|
||||
<data format="genetrack" name="genetrack" />
|
||||
<data format="bed" name="bed_out" />
|
||||
</outputs>
|
||||
|
||||
<help>
|
||||
This tool takes the input Fit Data and creates a peak and curve plot showing
|
||||
the reads and fitness on each basepair. Features can be plotted below as tracks.
|
||||
|
||||
-----
|
||||
|
||||
**Syntax**
|
||||
|
||||
- **Track Label** is the name of the generated track.
|
||||
- **Fit Data** are the datasets to calculate coverage/reads across basepairs and generate a curve.
|
||||
- **Features** are additional datasets (interval format) to be plotted below as tracks.
|
||||
|
||||
</help>
|
||||
</tool>
|
||||
@@ -0,0 +1,13 @@
|
||||
import sets, os
|
||||
from galaxy import eggs
|
||||
from galaxy import jobs
|
||||
from galaxy.tools.parameters import DataToolParameter
|
||||
|
||||
def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
|
||||
"""
|
||||
Copy data_label to genetrack.metadata.label
|
||||
"""
|
||||
out_data['genetrack'].metadata.label = param_dict['data_label']
|
||||
out_data['genetrack'].info = "Use the link below to view the custom track."
|
||||
out_data['bed_out'].info = ""
|
||||
|
||||
Reference in New Issue
Block a user