diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 431d9da7c95..391f7937663 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -82,6 +82,8 @@
+
+
diff --git a/lib/galaxy/datatypes/coverage.py b/lib/galaxy/datatypes/coverage.py
new file mode 100644
index 00000000000..4bd76425a71
--- /dev/null
+++ b/lib/galaxy/datatypes/coverage.py
@@ -0,0 +1,30 @@
+"""
+Coverage datatypes
+
+"""
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+import logging, os, sys, time, sets, tempfile, shutil
+import data
+from galaxy import util
+from galaxy.datatypes.sniff import *
+from galaxy.web import url_for
+from cgi import escape
+import urllib
+from bx.intervals.io import *
+from galaxy.datatypes import metadata
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.tabular import Tabular
+
+log = logging.getLogger(__name__)
+
+class LastzCoverage( Tabular ):
+ file_ext = "coverage"
+
+ MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter )
+ MetadataElement( name="positionCol", default=2, desc="Position column", param=metadata.ColumnParameter )
+ MetadataElement( name="forwardCol", default=3, desc="Forward or aggregate read column", param=metadata.ColumnParameter )
+ MetadataElement( name="reverseCol", desc="Optional reverse read column", param=metadata.ColumnParameter, optional=True, no_value=0 )
+ MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )
+
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index c27cce91188..1639e904964 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -3,7 +3,7 @@ Provides mapping between extensions and datatypes, mime-types, etc.
"""
import os
import logging
-import data, tabular, interval, images, sequence, qualityscore, genetics, xml
+import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks
import galaxy.util
from galaxy.util.odict import odict
@@ -97,12 +97,14 @@ class Registry( object ):
'bed' : interval.Bed(),
'binseq.zip' : images.Binseq(),
'blastxml' : xml.BlastXml(),
+ 'coverage' : coverage.LastzCoverage(),
'customtrack' : interval.CustomTrack(),
'csfasta' : sequence.csFasta(),
'fasta' : sequence.Fasta(),
'fastqsolexa' : sequence.FastqSolexa(),
'gff' : interval.Gff(),
- 'gff3' : interval.Gff3(),
+ 'gff3' : interval.Gff3(),
+ 'genetrack' : tracks.GeneTrack(),
'interval' : interval.Interval(),
'laj' : images.Laj(),
'lav' : sequence.Lav(),
diff --git a/lib/galaxy/datatypes/tracks.py b/lib/galaxy/datatypes/tracks.py
new file mode 100644
index 00000000000..1c5a9291bef
--- /dev/null
+++ b/lib/galaxy/datatypes/tracks.py
@@ -0,0 +1,30 @@
+"""
+Datatype classes for tracks/track views within galaxy.
+"""
+
+import data
+import logging
+import re
+from cgi import escape
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes import metadata
+import galaxy.model
+from galaxy import util
+from galaxy.web import url_for
+from sniff import *
+
+log = logging.getLogger(__name__)
+
+class GeneTrack( data.Binary ):
+ file_ext = "genetrack"
+
+ MetadataElement( name="hdf", default="data.hdf", desc="HDF DB", readonly=True, visible=True, no_value=0 )
+ MetadataElement( name="sqlite", default="features.sqlite", desc="SQLite Features DB", readonly=True, visible=True, no_value=0 )
+ MetadataElement( name="label", default="Custom", desc="Track Label", readonly=True, visible=True, no_value="Custom" )
+
+ def __init__(self, **kwargs):
+ super(GeneTrack, self).__init__(**kwargs)
+ self.add_display_app( 'genetrack', 'View in ', '', 'genetrack_link' )
+
+ def genetrack_link( self, dataset, type, app, base_url ):
+ return [('GeneTrack', url_for(controller='genetrack', action='index', dataset_id=dataset.id ))]
\ No newline at end of file
diff --git a/lib/galaxy/web/controllers/genetrack.py b/lib/galaxy/web/controllers/genetrack.py
new file mode 100644
index 00000000000..ae81a277cd4
--- /dev/null
+++ b/lib/galaxy/web/controllers/genetrack.py
@@ -0,0 +1,161 @@
+import time, glob, os
+
+import pkg_resources
+pkg_resources.require("GeneTrack")
+
+import atlas
+from atlas import sql
+from atlas import util as atlas_utils
+from atlas.web import formlib
+from mako import exceptions
+from mako.template import Template
+from mako.lookup import TemplateLookup
+from galaxy.web.base.controller import *
+
+pkg_resources.require( "Paste" )
+import paste.httpexceptions
+
+# SETUP Track Builders
+from mod454.trackbuilder import build_tracks
+import functools
+def twostrand_tracks( param=None, conf=None ):
+ return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='twostrand')
+def composite_tracks( param=None, conf=None ):
+ return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='composite')
+
+class BaseConf( object ):
+ """
+ Fake web_conf for atlas.
+ """
+ IMAGE_DIR = "static/genetrack/plots/"
+ LEVELS = [str(x) for x in [ 50, 100, 250, 500, 1000, 2500, 5000, 10000, 20000, 50000, 100000, 200000 ]]
+ ZOOM_LEVELS = zip(LEVELS, LEVELS)
+ PLOT_SETUP = [
+ ('comp-id', 'Composite' , 'genetrack/index.html', composite_tracks ),
+ ('two-id' , 'Two Strand', 'genetrack/index.html', twostrand_tracks ),
+ ]
+ PLOT_CHOICES = [ (id, name) for (id, name, page, func) in PLOT_SETUP ]
+ PLOT_MAPPER = dict( [ (id, (page, func)) for (id, name, page, func) in PLOT_SETUP ] )
+
+ def __init__(self, **kwds):
+ for key,value in kwds.items():
+ setattr( self, key, value)
+
+class WebRoot(BaseController):
+ @web.expose
+ def search(self, trans, word='', dataset_id=None, submit=''):
+ """
+ Default search page
+ """
+ data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
+ if not data:
+ raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
+ # the main configuration file
+ conf = BaseConf(
+ TITLE = "%s: %s" % (data.metadata.dbkey, data.metadata.label),
+ HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ),
+ SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ),
+ LABEL = data.metadata.label,
+ FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
+ PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
+ )
+ from atlas import hdf
+ db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
+ conf.CHROM_FIELDS = [(x,x) for x in hdf.GroupData(db=db, name=conf.LABEL).labels]
+ db.close()
+
+ param = atlas.Param( word=word )
+ # search with features based on param.feature
+
+ # search for a given
+ session = sql.get_session( conf.SQL_URI )
+
+ if param.word:
+ def search_query( word, text ):
+ query = session.query(sql.Feature).filter( "name LIKE :word or freetext LIKE :text" ).params(word=word, text=text)
+ query = list(query[:20])
+ return query
+
+ # a little heuristics to match most likely target
+ targets = [
+ (param.word+'%', 'No match'), # match beginning
+ ('%'+param.word+'%', 'No match'), # match name anywhere
+ ('%'+param.word+'%', '%'+param.word+'%'), # match json anywhere
+ ]
+ for word, text in targets:
+ query = search_query( word=word, text=text)
+ if query:
+ break
+ else:
+ query = []
+
+ return trans.fill_template_mako('genetrack/search.html', param=param, query=query, dataset_id=dataset_id)
+
+ @web.expose
+ def index(self, trans, dataset_id=None, **kwds):
+ """
+ Main request handler
+ """
+ data = trans.app.model.HistoryDatasetAssociation.get( dataset_id )
+ if not data:
+ raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) )
+ # the main configuration file
+ conf = BaseConf(
+ TITLE = "%s: %s" % (data.metadata.dbkey, data.metadata.label),
+ HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ),
+ SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ),
+ LABEL = data.metadata.label,
+ FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
+ PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
+ )
+ from atlas import hdf
+ db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
+ conf.CHROM_FIELDS = [(x,x) for x in hdf.GroupData(db=db, name=conf.LABEL).labels]
+ db.close()
+
+ # generate a new form based on the configuration
+ form = formlib.main_form( conf )
+
+ # clear the tempdir every once in a while
+ atlas_utils.clear_tempdir( dir=conf.IMAGE_DIR, days=1, chance=10)
+
+ incoming = form.defaults()
+ incoming.update( kwds )
+
+ # manage the zoom and pan requests
+ incoming = formlib.zoom_change( kdict=incoming, levels=conf.LEVELS)
+ incoming = formlib.pan_view( kdict=incoming )
+
+ # process the form
+ param = atlas.Param( **incoming )
+ form.process( incoming )
+
+ if kwds and form.isSuccessful():
+ # adds the sucessfull parameters
+ param.update( form.values() )
+
+ # if it was a search word not a number go to search page
+ try:
+ center = int( param.feature )
+ except ValueError:
+ # go and search for these
+ return trans.response.send_redirect( web.url_for( controller='genetrack', action='search', word=param.feature, dataset_id=dataset_id ) )
+
+ # keep image at a sane size
+ param.width = min( [2000, int(param.img_size)] )
+
+ # get the template and the function used to generate the tracks
+ tmpl_name, track_maker = conf.PLOT_MAPPER[param.plot]
+
+ if track_maker is not None:
+ # generate the name that the image will be stored at
+ fname, fpath = atlas_utils.make_tempfile( dir=conf.IMAGE_DIR, suffix='.png')
+ param.fname = fname
+
+ # generate the track
+ track_chart = track_maker( param=param, conf=conf )
+ track_chart.save(fname=fpath)
+
+ return trans.fill_template_mako(tmpl_name, conf=conf, form=form, param=param, dataset_id=dataset_id)
+
+
diff --git a/scripts/paster.py b/scripts/paster.py
index 7624257a665..446cb9de90b 100755
--- a/scripts/paster.py
+++ b/scripts/paster.py
@@ -12,7 +12,7 @@ assert sys.version_info[:2] >= ( 2, 4 )
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
-
+print sys.path
from galaxy import eggs
import pkg_resources
diff --git a/static/genetrack/genetrack.css b/static/genetrack/genetrack.css
new file mode 100644
index 00000000000..668300be06d
--- /dev/null
+++ b/static/genetrack/genetrack.css
@@ -0,0 +1,78 @@
+
+body {
+ font-family: "Trebuchet MS", Arial, tahoma, sans-serif;
+ font-size: 14px;
+ line-height: 1.6em;
+ margin: 0;
+ padding: 0;
+ border-top: 9px solid #CCD9FF;
+}
+
+/* Error message style */
+.error{
+ background: #FFFF66;
+}
+
+/* Error message style */
+.message{
+ background: #33FF66;
+}
+
+/* Odd data row in the table */
+.selected {
+ background-color: #FFFFCC;
+}
+
+.nav_button{
+ background-color:#EEEEEE;
+ border:1px solid;
+ color: #000000;
+}
+
+.nav_button:hover{
+ background-color:#000000;
+ border:1px solid;
+ color: #FFFFFF;
+}
+
+.grey {
+ background-color: #EFEFEF;
+}
+
+.odd {
+ background-color: #ECECEC;
+}
+
+.even {
+ background-color: #FFFFFF;
+}
+
+/* Text table style */
+.data_table {
+ border: 1px solid #CCCCCC;
+ background-color: white;
+}
+
+/* Footer is added to every page */
+#footer {
+ background: #EFEFEF;
+ text-align:center;
+ padding:.2em;
+ border-top: 1px solid #CCD9FF;
+ border-bottom: 1px solid #CCD9FF;
+ clear: both;
+}
+
+#footer p {
+ font-size:.94em; line-height:2em; color:#cccccc; margin: 0;
+ }
+
+#tag {
+ font-size:.80em; margin: 4px; padding: 2px;
+ }
+
+
+#footer img {
+ vertical-align: middle; margin-left: 3px; padding-bottom: 2px;
+}
+
diff --git a/static/genetrack/genetrack.js b/static/genetrack/genetrack.js
new file mode 100644
index 00000000000..be88d107ab8
--- /dev/null
+++ b/static/genetrack/genetrack.js
@@ -0,0 +1,79 @@
+var cookie_name = "genetrack_ui"
+var now = new Date();
+now.setTime(now.getTime() + 365 * 24 * 60 * 60 * 1000);
+
+// 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));
+}
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index f46c9cef558..47cf0c1e734 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -11,7 +11,6 @@
-
@@ -302,4 +301,7 @@
+
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index e3aabf57243..f29d5fb7168 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -82,7 +82,7 @@
-
+
lastz
diff --git a/tools/visualization/genetrack.py b/tools/visualization/genetrack.py
new file mode 100644
index 00000000000..bd27d5df4d2
--- /dev/null
+++ b/tools/visualization/genetrack.py
@@ -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)
+
\ No newline at end of file
diff --git a/tools/visualization/genetrack.xml b/tools/visualization/genetrack.xml
new file mode 100644
index 00000000000..65c5f519b31
--- /dev/null
+++ b/tools/visualization/genetrack.xml
@@ -0,0 +1,53 @@
+
+
+ Track creator/viewer
+
+
+
+
+
+
+ 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}
+
+
+
+
+ [a-zA-Z0-9]{0,25}
+
+
+
+
+
+ [a-zA-Z0-9]{0,25}
+
+
+
+
+
+
+
+
+
+
+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.
+
+
+
diff --git a/tools/visualization/genetrack_code.py b/tools/visualization/genetrack_code.py
new file mode 100644
index 00000000000..9c20ec27b73
--- /dev/null
+++ b/tools/visualization/genetrack_code.py
@@ -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 = ""
+
\ No newline at end of file