- Performance of indexers much improved.

- Indexing for tracks done in background with a visual treatment done to Trackster

- DB builds can be uploaded by a user (chromInfo/len extension).

- TODO: Add ability to change the dbkey of a dataset to any arbitrary string value.

datatypes_conf.xml.sample

@@ -8,6 +8,9 @@
       <converter file="interval_to_coverage.xml" target_datatype="coverage"/>
     </datatype>
     <datatype extension="binseq.zip" type="galaxy.datatypes.images:Binseq" mimetype="application/zip" display_in_upload="true"/>
+    <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true">
+      <!-- no converters yet -->
+    </datatype>
     <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true">
       <indexer file="coverage.xml" />
     </datatype>
@@ -31,7 +34,7 @@
     <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
       <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
-      <indexer file="interval.xml" />
+      <indexer file="interval_awk.xml" />
     </datatype>
     <datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
     <datatype extension="laj" type="galaxy.datatypes.images:Laj"/>

lib/galaxy/datatypes/data.py

@@ -40,7 +40,7 @@ class Data( object ):
     __metaclass__ = DataMeta
     
     """Add metadata elements"""
-    MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.SelectParameter, multiple=False, values=util.dbnames, no_value="?" )
+    MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.DBKeyParameter, multiple=False, no_value="?" )
     
     """Stores the set of display applications, and viewing methods, supported by this datatype """
     supported_display_apps = {}
@@ -242,7 +242,7 @@ class Data( object ):
     def after_edit( self, dataset ):
         """This function is called on the dataset after metadata is edited."""
         dataset.clear_associated_files( metadata_safe = True )
-
+    
     @property
     def has_resolution(self):
         return False

lib/galaxy/datatypes/indexers/coverage.py

@@ -37,7 +37,7 @@ def write_chrom(max, out_base, instream):
     os.rename( fname+".npy", fname )
 
     # Write average
-    for window in 10, 100, 1000, 10000:
+    for window in 10, 100, 1000, 10000, 100000:
         input = scores.copy()
         size = len( input )
         input.resize( ( ( size / window ), window ) )

lib/galaxy/datatypes/indexers/interval.awk

@@ -0,0 +1,43 @@
+BEGIN {
+    # from galaxy.utils
+    mapped_chars[">"] = "__gt__"
+    mapped_chars["<"] = "__lt__"
+    mapped_chars["'"] = "__sq__"
+    mapped_chars["\""] = "__dq__"
+    mapped_chars["\\["] = "__ob__"
+    mapped_chars["\\]"] = "__cb__"
+    mapped_chars["\\{"] = "__oc__"
+    mapped_chars["\\}"] = "__cc__"
+    mapped_chars["@"] = "__at__"
+    # additional, not in galaxy.utils
+    mapped_chars["/"] = "__fs__"
+    mapped_chars["^manifest\.tab$"] = "__manifest.tab__"
+}
+function escape_filename( name )
+{
+    for( char in mapped_chars ) {
+	gsub( char, mapped_chars[char], name )
+    }
+    return name
+}
+!_[$chrom]++ {
+    # close files only when we switch to a new one.
+    fn && close(fn)
+    fn = storepath "/" escape_filename($1) }
+{   
+    print $0 >> fn;
+    # the || part is needed to catch 0 length chromosomes, which
+    # should never happen but...
+    if ($end > chroms[$chrom] || !chroms[$chrom])
+	chroms[$chrom] = $end }
+END { 
+    fn = storepath "/manifest.tab"
+    for( x in chroms ) {
+	# add line to manifest
+	print x "\t" chroms[x] >> fn
+	chromfile = storepath "/" escape_filename(x)
+	# sort in-place
+	system( "sort -f -n -k " chrom " -k " start " -k " end " -o " chromfile " " chromfile )
+	close(chromfile)
+    }
+}

lib/galaxy/datatypes/indexers/interval.py

@@ -29,13 +29,11 @@ def divide( intervals, out_path ):
         manifest[chrom] = max(manifest.get(chrom,0),line.end)
         if not lastchrom == chrom:
             if current_file:
-                current_file.flush()
                 current_file.close()
             current_file = open( os.path.join( out_path, "%s" % chrom), "a" )
         print >> current_file, "\t".join(line)
         lastchrom = chrom
     if current_file:
-        current_file.flush()
         current_file.close()
     return manifest
 

lib/galaxy/datatypes/indexers/interval_awk.xml

@@ -0,0 +1,16 @@
+<tool id="INDEXER_Interval_0" name="Index Interval for Track Viewer">
+  <!-- Used internally to generate track indexes -->
+  <command interpreter="awk -f">interval.awk 
+    chrom=${input_dataset.metadata.chromCol} start=${input_dataset.metadata.startCol}
+    end=${input_dataset.metadata.endCol} strand=${input_dataset.metadata.strandCol}
+    storepath=${store_path} 
+    $input_dataset 2&gt;&amp;1
+  </command>
+  <inputs>
+    <page>
+      <param format="interval" name="input_dataset" type="data" label="Choose intervals"/>
+    </page>
+   </inputs>
+  <help>
+  </help>
+</tool>

lib/galaxy/datatypes/indexers/wiggle.py

@@ -18,6 +18,8 @@ pkg_resources.require("numpy>=1.2.1")
 from numpy import *
 import tempfile
 import os
+from galaxy.tracks.store import sanitize_name
+
 
 def write_chrom(max, out_base, instream):
    
@@ -35,7 +37,7 @@ def write_chrom(max, out_base, instream):
     os.rename( fname+".npy", fname )
 
     # Write average
-    for window in 10, 100, 1000, 10000:
+    for window in 10, 100, 1000, 10000, 100000:
         input = scores.copy()
         size = len( input )
         input.resize( ( ( size / window ), window ) )
@@ -60,7 +62,7 @@ def main():
         LEN[chrom] = max2( LEN.get(chrom,0), pos+1 )
     for chrom, stream in chroms.items():
         stream.seek(0)
-        prefix = os.path.join(sys.argv[2], chrom)
+        prefix = os.path.join(sys.argv[2], sanitize_name(chrom))
         write_chrom( LEN[chrom], prefix, stream )
 
     manifest_file = open( os.path.join( sys.argv[2], "manifest.tab" ),"w" )

lib/galaxy/datatypes/interval.py

@@ -792,7 +792,7 @@ class Wiggle( Tabular ):
         # Determine appropriate resolution to plot ~1000 points
         resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
         # Restrict to valid range
-        resolution = min( resolution, 10000 )
+        resolution = min( resolution, 100000 )
         resolution = max( resolution, 1 )
         # Memory map the array (don't load all the data)
         data = numpy.load( data )
@@ -809,7 +809,7 @@ class Wiggle( Tabular ):
         # Determine appropriate resolution to plot ~1000 points
         resolution = math.ceil( 10 ** math.ceil( math.log10( range / 1000 ) ) )
         # Restrict to valid range
-        resolution = min( resolution, 10000 )
+        resolution = min( resolution, 100000 )
         resolution = max( resolution, 1 )
         return resolution
 

lib/galaxy/datatypes/metadata.py

@@ -289,7 +289,22 @@ class SelectParameter( MetadataParameter ):
         if value is None: return []
         if not isinstance( value, list ): return [value]
         return value
-    
+
+
+class DBKeyParameter( SelectParameter ):
+    def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd):
+        try:
+            values = kwd['trans'].db_builds
+        except AttributeError: pass
+        return super(DBKeyParameter, self).get_html_field( value, context, other_values, values, **kwd)
+
+    def get_html( self, value=None, context={}, other_values={}, values=None, **kwd):
+        try:
+            values = kwd['trans'].db_builds
+        except AttributeError: pass
+        return super(DBKeyParameter, self).get_html( value, context, other_values, values, **kwd)
+
+
 class RangeParameter( SelectParameter ):
     def __init__( self, spec ):
         SelectParameter.__init__( self, spec )

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, coverage, tracks
+import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo
 import galaxy.util
 from galaxy.util.odict import odict
 

lib/galaxy/tools/actions/__init__.py

@@ -107,6 +107,7 @@ class DefaultToolAction( object ):
         out_data = {}
         # Collect any input datasets from the incoming parameters
         inp_data = self.collect_input_datasets( tool, incoming, trans )
+
         # Deal with input dataset names, 'dbkey' and types
         input_names = []
         input_ext = 'data'
@@ -119,6 +120,16 @@ class DefaultToolAction( object ):
                 data = NoneDataset( datatypes_registry = trans.app.datatypes_registry )
             if data.dbkey not in [None, '?']:
                 input_dbkey = data.dbkey
+
+        # Collect chromInfo dataset and add as parameters to incoming
+        db_datasets = {}
+        db_dataset = trans.db_dataset_for( input_dbkey )
+        if db_dataset:
+            db_datasets[ "chromInfo" ] = db_dataset
+            incoming[ "chromInfo" ] = db_dataset.file_name
+        else:
+            incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey )
+        inp_data.update( db_datasets )
         
         # Determine output dataset permission/roles list
         existing_datasets = [ inp for inp in inp_data.values() if inp ]

lib/galaxy/tools/actions/upload.py

@@ -21,7 +21,7 @@ class UploadToolAction( object ):
     def execute( self, tool, trans, incoming={}, set_output_hid = True ):
         data_file = incoming['file_data']
         file_type = incoming['file_type']
-        dbkey = incoming['dbkey']
+        dbkey = incoming['other_dbkey'] or incoming['dbkey']
         url_paste = incoming['url_paste']
         is_multi_byte = False
         space_to_tab = False 

lib/galaxy/tools/parameters/basic.py

@@ -657,7 +657,7 @@ class GenomeBuildParameter( SelectToolParameter ):
     
     >>> # Create a mock transcation with 'hg17' as the current build
     >>> from galaxy.util.bunch import Bunch
-    >>> trans = Bunch( history=Bunch( genome_build='hg17' ) )
+    >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames )
     
     >>> p = GenomeBuildParameter( None, XML( 
     ... '''
@@ -692,10 +692,10 @@ class GenomeBuildParameter( SelectToolParameter ):
     """
     def get_options( self, trans, other_values ):
         last_used_build = trans.history.genome_build
-        for dbkey, build_name in util.dbnames:
+        for dbkey, build_name in trans.db_builds:
             yield build_name, dbkey, ( dbkey == last_used_build )
     def get_legal_values( self, trans, other_values ):
-        return set( dbkey for dbkey, _ in util.dbnames )
+        return set( dbkey for dbkey, _ in trans.db_builds )
 
 class ColumnListParameter( SelectToolParameter ):
     """

lib/galaxy/tracks/store.py

@@ -1,5 +1,17 @@
 import os
+import re
 from string import Template
+from galaxy.util import sanitize_text
+
+# extra mappings/escape to keep users from traversing around the
+# filesystem and wreaking havoc
+extra_mappings = { r"/": "__fs__", r"^manifest.tab$": "__manifest.tab__" }
+
+def sanitize_name( name ):
+    name = sanitize_text( name )
+    for key, value in extra_mappings.items():
+        name = re.sub( key, value, name )
+    return name
 
 class TemplateSubber( object ):
     def __init__(self, obj):
@@ -56,7 +68,7 @@ class TrackStore( object ):
         fd.close()
         
     def _get_object_path( self, chrom, resolution ):
-        object_name = chrom
+        object_name = sanitize_name(chrom)
         if resolution: object_name += "_%d" % resolution
         return os.path.join( self.path, object_name )
 

lib/galaxy/web/controllers/root.py

@@ -234,11 +234,15 @@ class RootController( BaseController ):
                     if spec.get("readonly"):
                         continue
                     optional = params.get("is_"+name, None)
+                    other = params.get("or_"+name, None)
                     if optional and optional == 'true':
                         # optional element... == 'true' actually means it is NOT checked (and therefore omitted)
                         setattr(data.metadata, name, None)
                     else:
-                        setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
+                        if other:
+                            setattr( data.metadata, name, other )
+                        else:
+                            setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) )
 
                 data.datatype.after_edit( data )
                 trans.app.model.flush()

lib/galaxy/web/controllers/tracks.py

@@ -1,13 +1,11 @@
-from mako import exceptions
-from mako.template import Template
-from mako.lookup import TemplateLookup
+import math
+
+import mimeparse
+from galaxy.tracks import messages
+from galaxy.util.json import to_json_string
 from galaxy.web.base.controller import *
 from galaxy.web.framework import simplejson
-from galaxy import web
-from galaxy.tracks import messages
-import mimeparse
-from galaxy.util.json import to_json_string
-import math
+
 
 class MultiResponse(object):
     """
@@ -82,18 +80,19 @@ class WebRoot( BaseController ):
     def build( self, trans, **kwargs ):
         trans.session["track_sets"] = list(kwargs.keys())
         trans.session.save()
-        waiting = False
-        for id, value in kwargs.items():
-            status = self.data_handler( trans, id )
-            if status == messages.PENDING:
-                waiting = True
-        if not waiting:
-            return trans.response.send_redirect( web.url_for( controller='tracks', action='chroms', dbkey=trans.session["track_dbkey"]) )
-        return trans.fill_template( 'tracks/build.mako' )
+        #waiting = False
+        #for id, value in kwargs.items():
+        #    status = self.data_handler( trans, id )
+        #    if status == messages.PENDING:
+        #        waiting = True
+        #if not waiting:
+        return trans.response.send_redirect( web.url_for( controller='tracks/', action='index', chrom="" ) )
+        #return trans.fill_template( 'tracks/build.mako' )
         
     @web.expose
     def index(self, trans, **kwargs):
         tracks = []
+        dbkey = ""
         for track in trans.session["track_sets"]:
             dataset = trans.app.model.HistoryDatasetAssociation.get( track )
             tracks.append({
@@ -101,17 +100,23 @@ class WebRoot( BaseController ):
                     "name": dataset.name,
                     "id": dataset.id
                     })
+            dbkey = dataset.dbkey
         chrom = kwargs.get("chrom","")
         LEN = self.chroms_handler(trans, trans.session["track_dbkey"]).get(chrom,0)
         return trans.fill_template( 'tracks/index.mako', 
-                                    tracks=tracks, chrom=chrom, 
+                                    tracks=tracks, chrom=chrom, dbkey=dbkey,
                                     LEN=LEN )
 
     def chroms_handler(self, trans, dbkey ):
-        db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey )
+        db_manifest = trans.db_dataset_for( dbkey )
+        if not db_manifest:
+            db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey )
+        else:
+            db_manifest = db_manifest.file_name
         manifest = {}
         if os.path.exists( db_manifest ):
             for line in open( db_manifest ):
+                if line.startswith("#"): continue
                 line = line.rstrip("\r\n")
                 fields = line.split("\t")
                 manifest[fields[0]] = int(fields[1])

lib/galaxy/web/framework/__init__.py

@@ -547,6 +547,31 @@ class UniverseWebTransaction( base.DefaultWebTransaction ):
         template = Template( source=template_string,
                              searchList=[context or kwargs, dict(caller=self)] )
         return str(template)
+
+    @property
+    def db_builds( self ):
+        """
+        Returns the builds defined by galaxy and the builds defined by
+        the user (chromInfo in history).
+        """
+        dbnames = list()
+        datasets = self.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=self.history.id, extension="len").all()
+        if len(datasets) > 0:
+            dbnames.append( (util.dbnames.default_value, '--------- User Defined Builds ----------') )
+        for dataset in datasets:
+            dbnames.append( (dataset.dbkey, dataset.name) )
+        dbnames.extend( util.dbnames )
+        return dbnames
+        
+    def db_dataset_for( self, dbkey ):
+        """
+        Returns the db_file dataset associated/needed by `dataset`, or `None`.
+        """
+        datasets = self.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=self.history.id, extension="len").all()
+        for ds in datasets:
+            if dbkey == ds.dbkey:
+                return ds
+        return None
         
 class FormBuilder( object ):
     """

static/scripts/trackster.js

@@ -85,7 +85,7 @@ $.extend( TiledTrack.prototype, Track.prototype, {
 
         var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) );
         resolution = Math.max( resolution, 1 );
-        resolution = Math.min( resolution, 10000 );
+        resolution = Math.min( resolution, 100000 );
 
 	var parent_element = $("<div style='position: relative;'></div>");
         this.content_div.children( ":first" ).remove();
@@ -152,10 +152,20 @@ $.extend( DataCache.prototype, {
             var low = position * DENSITY * resolution;
             var high = ( position + 1 ) * DENSITY * resolution;
             cache[resolution][position] = { state: "loading" };
-            $.getJSON( "data" + this.type, { chr: this.view.chr, low: low, high: high, dataset_id: this.track.dataset_id }, function ( data ) {
-                cache[resolution][position] = { state: "loaded", values: data };
-                $(document).trigger( "redraw" );
-            });
+	    // use closure to preserve this and parameters for getJSON
+	    var fetcher = function (ref) {
+	      return function () {
+		$.getJSON( "data" + ref.type, { chr: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) {
+		  if( data == "pending" ) {
+		    setTimeout( fetcher, 5000 );
+		  } else {
+		    cache[resolution][position] = { state: "loaded", values: data };
+		  }
+		  $(document).trigger( "redraw" );
+		});
+	      };
+	    }(this);
+	    fetcher();
         }
 	return cache[resolution][position];
     }
@@ -288,8 +298,11 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
 
         var chunk = this.cache.get( resolution, tile_index );
         if ( chunk.state == "loading" ) {
-            return null;
-        }
+	  parent_element.addClass("loading");
+          return null;
+        } else {
+	  parent_element.removeClass("loading");
+	}
         var values = chunk.values;
 
         for ( var index in values ) {

static/trackster.css

@@ -85,7 +85,10 @@ body {
 }
 
 .loading {
-    background: #DDDDDD;
+    background-image: url("/static/images/loading_large_white_bg.gif");
+    background-position: center center;
+    background-repeat: no-repeat;
+    min-height: 100px;
 }
 
 .label-track .label {

templates/dataset/edit_attributes.mako

@@ -46,7 +46,7 @@
                             ${spec.desc}:
                         </label>
                         <div style="float: left; width: 250px; margin-right: 10px;">
-                            ${data.metadata.get_html_by_name( name )}
+                            ${data.metadata.get_html_by_name( name, trans=trans )}
                         </div>
                         <div style="clear: both"></div>
                     </div>

templates/tracks/index.mako

@@ -17,18 +17,19 @@ ${parent.stylesheets()}
 ${parent.late_javascripts()}
 <script type="text/javascript" src="/static/scripts/jquery.event.drag.js"></script>
 <script type="text/javascript" src="/static/scripts/trackster.js"></script>
-<script>
+<script type="text/javascript">
 
-    var view = new View( "${chrom}", ${LEN}, 0, ${LEN} );
+    var view = new View( "${chrom}", ${LEN}, 0, ${max(LEN,1)} );
     var tracks = new TrackLayout( view );
-
+    var dbkey = "${dbkey}";
+    
     $(function() {
         
         tracks.add( new LabelTrack( view, $("#viewport" ) ) );
     %for track in tracks:
         tracks.add( new ${track["type"]}( "${track["name"]}", view, $("#viewport" ), ${track["id"]} ) );
     %endfor
-                
+        
         $(document).bind( "redraw", function( e ) {
             tracks.redraw();
         });
@@ -56,9 +57,43 @@ ${parent.late_javascripts()}
             view.high = new_high;
             tracks.redraw();
         });
-
         tracks.redraw();
+        load_chroms();
     });
+
+    var load_chroms = function () {
+      var fetcher = function (ref) {
+	return function () {
+	  $.getJSON( "chroms", { dbkey: dbkey }, function ( data ) {
+	    // Hacky - check length of "object"
+	    var chrom_length = 0;
+	    for (key in data) chrom_length++;
+	    if( chrom_length == 0 ) {
+	      setTimeout( fetcher, 5000 );
+	    } else {
+	      var chrom_options = '';
+	      for (key in data) {
+                if( key == view.chr ) {
+                  chrom_options += '<option value="' + key + '" selected="true">' + key + '</option>';                  
+                } else {
+                  chrom_options += '<option value="' + key + '">' + key + '</option>';
+                }
+	      }
+	      $("#chrom").html(chrom_options);
+              $("#chrom").bind( "change", function ( e ) {
+		$("#chr").submit();
+	      });
+              if( view.chr == "" ) {
+	       $("#chrom option:first").attr("selected", true);
+	       $("#chrom").trigger( "change" );
+              }
+	    }
+	  });
+	};
+      }(this);
+      fetcher();
+    };
+
 </script>
 </%def>
 
@@ -79,11 +114,14 @@ ${parent.late_javascripts()}
     <div id="nav">
 
         <div id="nav-controls">
+	<form name="chr" id="chr" method="GET">
         <a href="#" onclick="javascript:view.left(5);tracks.redraw();">&lt;&lt;</a>
         <a href="#" onclick="javascript:view.left(2);tracks.redraw();">&lt;</a>
-    
-        <span style="display: inline-block; width: 30em; text-align: center;">Viewing ${chrom}:<span id="low">0</span>-<span id="high">180857866</span></span>
-
+	  <span style="display: inline-block; width: 30em; text-align: center;">Viewing
+	    <select id="chrom" name="chrom">
+	      <option value="">loading</option>
+	    </select>
+	    <span id="low">0</span>-<span id="high">180857866</span></span>
         <span style="display: inline-block; width: 10em;">
         <a href="#" onclick="javascript:view.zoom_in(2);tracks.redraw();">+</a>
         <a href="#" onclick="javascript:view.zoom_out(2);tracks.redraw();">-</a>
@@ -91,6 +129,7 @@ ${parent.late_javascripts()}
 
         <a href="#" onclick="javascript:view.right(2);tracks.redraw();">&gt;</a>
         <a href="#" onclick="javascript:view.right(5);tracks.redraw();">&gt;&gt;</a>
+	</form>
         </div>
         
     </div>

tools/data_source/upload.xml

@@ -21,6 +21,7 @@
       </options>
     </param>
     <param name="dbkey" type="genomebuild" label="Genome" />
+    <param name="other_dbkey" type="text" label="Or user-defined Genome" />
   </inputs>
   <help>
   

tools/new_operations/complement.xml

@@ -1,6 +1,6 @@
 <tool id="gops_complement_1" name="Complement">
   <description>intervals of a query</description>
-  <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len $allchroms</command>
+  <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command>
   <inputs>
     <param format="interval" name="input1" type="data">
       <label>Complement regions of</label>
@@ -58,4 +58,4 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano
 .. image:: ../static/operation_icons/gops_complement.gif
 
 </help>
-</tool>
+</tool>