Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

lib/galaxy/jobs/__init__.py

@@ -256,11 +256,10 @@ class JobWrapper( object ):
         incoming = self.tool.params_from_strings( incoming, self.app )
         # Do any validation that could not be done at job creation
         self.tool.handle_unvalidated_param_values( incoming, self.app )
-        # Resore input / output data lists
+        # Restore input / output data lists
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
-        # add some useful session info to param_dict via incoming - ross august 2007
-        # these can be passed on the commandline if wanted as $userId $userEmail
+        # These can be passed on the command line if wanted as $userId $userEmail
         if job.history.user: # check for anonymous user!
              userId = '%d' % job.history.user.id
              userEmail = str(job.history.user.email)
@@ -271,10 +270,7 @@ class JobWrapper( object ):
         incoming['userEmail'] = userEmail
         # Build params, done before hook so hook can use
         param_dict = self.tool.build_param_dict( incoming, inp_data, out_data )
-        # Run the before queue ("exec_before_job") hook "trans" is no
-        # longer available to this hook, and has been replaced with
-        # app - 5/31/2007, by INS
-        # job added so we can get at the user if needed 14/august/2007 ross
+        # Run the before queue ("exec_before_job") hook
         self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data, 
                              out_data=out_data, tool=self.tool, param_dict=incoming)
         mapping.context.current.flush()
@@ -287,8 +283,8 @@ class JobWrapper( object ):
         # FIXME: for now, tools get Galaxy's lib dir in their path
         if self.command_line and self.command_line.startswith( 'python' ):
             self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root
-        # command_line won't actually be set in the db until finish unless you do it here
-        # We need it in the db to be able to restart jobs -ndc
+        # We need command_line persisted to the db in order for Galaxy to re-queue the job
+        # if the server was stopped and restarted before the job finished
         job.command_line = self.command_line
         job.flush()
         # Return list of all extra files

lib/galaxy/tools/__init__.py

@@ -282,9 +282,6 @@ class Tool:
         self.parse_inputs( root )
         # Parse tool help
         self.parse_help( root )
-        # FIXME: This is not used anywhere, what does it do?
-        # url redirection to ougoings
-        self.redir_url  = root.find("url")
         # Description of outputs produced by an invocation of the tool
         self.outputs = {}
         out_elem = root.find("outputs")
@@ -1040,7 +1037,7 @@ class Tool:
             return
         try:                
             # Substituting parameters into the command
-            command_line = fill_template( self.command, context=param_dict ) 
+            command_line = fill_template( self.command, context=param_dict )
             # Remove newlines from command line
             command_line = command_line.replace( "\n", " " ).replace( "\r", " " )
         except Exception, e:

lib/galaxy/tools/actions/__init__.py

@@ -64,21 +64,13 @@ class DefaultToolAction( object ):
         return input_datasets
     
     def execute(self, tool, trans, incoming={}, set_output_hid = True ):
-        out_data   = {}
-        
+        out_data = {}
         # Collect any input datasets from the incoming parameters
         inp_data = self.collect_input_datasets( tool, incoming, trans )
-        
-        # Deal with input metadata, 'dbkey', names, and types
-        
-        # FIXME: does this need to modify 'incoming' or should this be 
-        #        moved into 'build_param_dict'? Is this just about getting the
-        #        metadata into the command line?
-        # NEED TO FIX THIS SOON.
+        # Deal with input dataset names, 'dbkey' and types
         input_names = []
         input_ext = 'data'
         input_dbkey = incoming.get( "dbkey", "?" )
-        input_meta = Bunch()
         for name, data in inp_data.items():
             if data:
                 input_names.append( 'data %s' % data.hid )
@@ -87,15 +79,6 @@ class DefaultToolAction( object ):
                 data = NoneDataset( datatypes_registry = trans.app.datatypes_registry )
             if data.dbkey not in [None, '?']:
                 input_dbkey = data.dbkey
-            for meta_key, meta_value in data.metadata.items():
-                if meta_value is not None:
-                    meta_value = str(data.datatype.metadata_spec[meta_key].wrap(meta_value, data))
-                    meta_key = '%s_%s' % (name, meta_key)
-                    incoming[meta_key] = meta_value
-                else:
-                    incoming_key = '%s_%s' % (name, meta_key)
-                    incoming[incoming_key] = data.datatype.metadata_spec[meta_key].no_value
-
         # Build name for output datasets based on tool name and input names
         if len( input_names ) == 1:
             on_text = input_names[0]
@@ -186,16 +169,13 @@ class DefaultToolAction( object ):
         # Create the job object
         job = trans.app.model.Job()
         job.session_id = trans.get_galaxy_session( create=True ).id
-        if trans.get_history() is not None:
-            job.history_id = trans.get_history().id
+        job.history_id = trans.history.id
         job.tool_id = tool.id
         try:
-            # For backward compatability, some tools may not have versions yet.
+            # For backward compatibility, some tools may not have versions yet.
             job.tool_version = tool.version
         except:
             job.tool_version = "1.0.0"
-        ## job.command_line = command_line
-        ## job.param_filename = param_filename
         # FIXME: Don't need all of incoming here, just the defined parameters
         #        from the tool. We need to deal with tools that pass all post
         #        parameters to the command as a special case.
@@ -212,6 +192,5 @@ class DefaultToolAction( object ):
         
         # Queue the job for execution
         trans.app.job_queue.put( job.id, tool )
-        # IMPORTANT: keep the following event as is - we parse it for our session activity reports
         trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
         return out_data

test/base/twilltestcase.py

@@ -216,7 +216,7 @@ class TwillTestCase( unittest.TestCase ):
 
     def _assert_dataset_state( self, elem, state ):
         if elem.get( 'state' ) != state:
-            errmsg = "Expecting dataset state '%s' but is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() )
+            errmsg = "Expecting dataset state '%s', but state is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() )
             errmsg += "---------------------- >> begin tool stderr << -----------------------\n"
             errmsg += self.get_job_stderr( elem.get( 'id' ) ) + "\n"
             errmsg += "----------------------- >> end tool stderr << ------------------------\n"

tool_conf.xml.main

@@ -85,9 +85,9 @@
     <tool file="maf/maf_limit_to_species.xml"/>
     <tool file="maf/maf_limit_size.xml"/>
     <tool file="maf/maf_by_block_number.xml"/>
+    <tool file="maf/maf_filter.xml"/>
     <!--    
     <tool file="maf/maf_reverse_complement.xml"/>
-    <tool file="maf/maf_filter.xml"/> 
     -->
   </section>
   <section name="Get Genomic Scores" id="scores">
@@ -107,6 +107,7 @@
     <tool file="new_operations/join.xml" />
     <tool file="new_operations/get_flanks.xml" />
     <tool file="new_operations/flanking_features.xml" />
+    <tool file="annotation_profiler/annotation_profiler.xml" />
   </section>
   <section name="Statistics" id="stats">
     <tool file="stats/gsummary.xml" />

tools/annotation_profiler/annotation_profiler.xml

@@ -1,6 +1,6 @@
 <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0">
   <description>for a set of genomic intervals</description>
-  <command interpreter="python2.4">annotation_profiler_for_interval.py -i $input1 -c $input1_chromCol -s $input1_startCol -e $input1_endCol -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command>
+  <command interpreter="python2.4">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command>
   <inputs>
     <param format="interval" name="input1" type="data" label="Choose Intervals">
       <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>

tools/encode/gencode_partition.xml

@@ -1,6 +1,6 @@
 <tool id="gencode_partition1" name="Gencode Partition">
   <description>an interval file</description>
-  <command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol</command>
+  <command interpreter="python">split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command>
   <inputs>
     <param name="input1" type="data" format="interval" label="File to Partition"/>
   </inputs>

tools/encode/random_intervals.xml

@@ -1,6 +1,6 @@
 <tool id="random_intervals1" name="Random Intervals">
 <description>create a random set of intervals</description>
-  <command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 $input2_chromCol $input2_startCol $input2_endCol $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
+  <command interpreter="python">random_intervals_no_bits.py $regions $input2 $input1 $out_file1 ${input2.metadata.chromCol} ${input2.metadata.startCol} ${input2.metadata.endCol} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} $use_mask $strand_overlaps ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <param name="input1" type="data" format="interval" label="File to Mimick">
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16 or hg17. Click the pencil icon in your history item to set the genome build."/>
@@ -21,6 +21,7 @@
         <column name="value" index="1"/>
         <column name="dbkey" index="0"/>
         <filter type="data_meta" ref="input1" key="dbkey" column="0" />
+        <validator type="no_options" message="This tool currently only works with ENCODE data from genome builds hg16 or hg17."/>
       </options>
     </param> 
   </inputs>
@@ -31,7 +32,7 @@
 
 .. class:: warningmark
 
-This tool currently only works with data from genome builds hg16 or hg17.
+This tool currently only works with ENCODE data from genome builds hg16 or hg17.
 
 -----
 

tools/encode/split_by_partitions.py

@@ -57,7 +57,7 @@ def main():
     try:
         strandCol = int( sys.argv[7] )-1
     except:
-        stop_err( "Bad strand column: %s" % ( str( sys.argv[7] ) ) )
+        strandCol = -1
     
     line_count = 0
     skipped_lines = 0

tools/extract/extract_genomic_dna.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 """
-usage: extract_genomic_dna.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey $out_format GALAXY_DATA_INDEX_DIR
+usage: extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format GALAXY_DATA_INDEX_DIR
 by Wen-Yu Chung
 """
 from galaxy import eggs

tools/extract/extract_genomic_dna.xml

@@ -1,6 +1,6 @@
 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.1.0">
   <description>using coordinates from assembled/unassembled genomes</description>
-  <command interpreter="python">extract_genomic_dna.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command>
+  <command interpreter="python">extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query">
       <validator type="unspecified_build" />

tools/extract/phastOdds/phastOdds_tool.xml

@@ -1,6 +1,6 @@
 <tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0">
   <description>for each interval</description>
-  <command interpreter="python">get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output $input_chromCol $input_startCol $input_endCol</command>
+  <command interpreter="python">get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol}</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Interval file">
       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>

tools/maf/interval2maf.xml

@@ -1,8 +1,8 @@
 <tool id="Interval2Maf1" name="Extract MAF blocks">
   <description>given a set of genomic intervals</description>
   <command interpreter="python">
-    #if $maf_source_type.maf_source == "user":#interval2maf.py --dbkey=$input1_dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafFile=$maf_source_type.mafFile --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
-    #else:#interval2maf.py --dbkey=$input1_dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
+    #if $maf_source_type.maf_source == "user":#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
+    #else:#interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc
     #end if
   </command>
   <inputs>

tools/maf/interval2maf_pairwise.xml

@@ -1,6 +1,6 @@
 <tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks">
   <description>given a set of genomic intervals</description>
-  <command interpreter="python">interval2maf.py --dbkey=$input1_dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command>
+  <command interpreter="python">interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command>
   <inputs>
     <param name="input1" type="data" format="interval" label="Interval File">
       <validator type="unspecified_build" />

tools/maf/interval_maf_to_merged_fasta.xml

@@ -1,7 +1,7 @@
 <tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks">
   <description>given a set of genomic intervals</description>
-  <command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --interval_file=$input1 --output_file=$out_file1 --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
-#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
+  <command interpreter="python">#if $maf_source_type.maf_source == "user":#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
+#else:#interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR}
 #end if
   </command>
   <inputs>

tools/maf/maf_stats.xml

@@ -3,9 +3,9 @@
   <command interpreter="python">
     maf_stats.py
     #if $maf_source_type.maf_source == "user":
-      $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol $summary
+      $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
     #else:
-      $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol $summary
+      $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
     #end if
     ${GALAXY_DATA_INDEX_DIR}
   </command>

tools/new_operations/basecoverage.xml

@@ -1,6 +1,6 @@
 <tool id="gops_basecoverage_1" name="Base Coverage">
   <description>of all intervals</description>
-  <command interpreter="python">gops_basecoverage.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol</command>
+  <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
   <inputs>
     <param format="interval" name="input1" type="data">
       <label>Compute coverage for</label>

tools/new_operations/cluster.xml

@@ -1,6 +1,6 @@
 <tool id="gops_cluster_1" name="Cluster">
   <description>the intervals of a query</description>
-  <command interpreter="python">gops_cluster.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -d $distance -m $minregions -o $returntype</command>
+  <command interpreter="python">gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype</command>
   <inputs>
     <param format="interval" name="input1" type="data">
       <label>Cluster intervals of</label>

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 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_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 ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len $allchroms</command>
   <inputs>
     <param format="interval" name="input1" type="data">
       <label>Complement regions of</label>

tools/new_operations/concat.xml

@@ -1,6 +1,6 @@
 <tool id="gops_concat_1" name="Concatenate">
   <description>two queries into one query</description>
-  <command interpreter="python">gops_concat.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol $sameformat</command>
+  <command interpreter="python">gops_concat.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} $sameformat</command>
   <inputs>
     <param format="interval" name="input1" type="data" help="First query">
       <label>Concatenate</label>

tools/new_operations/coverage.xml

@@ -1,6 +1,6 @@
 <tool id="gops_coverage_1" name="Coverage">
   <description>of a set of intervals on second set of intervals</description>
-  <command interpreter="python">gops_coverage.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol</command>
+  <command interpreter="python">gops_coverage.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
   <inputs>
     <param format="interval" name="input1" type="data" help="First query">
       <label>What portion of</label>

tools/new_operations/flanking_features.xml

@@ -1,6 +1,6 @@
 <tool id="flanking_features_1" name="Fetch closest feature" version="2.0.0">
   <description>  for every interval</description>
-  <command interpreter="python">flanking_features.py $input1 $input2 $out_file1 $direction -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol</command>
+  <command interpreter="python">flanking_features.py $input1 $input2 $out_file1 $direction -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
   <inputs>
     <param format="interval" name="input1" type="data" label="For every interval in"/>
     <param format="interval" name="input2" type="data" label="Fetch features from"/>

tools/new_operations/get_flanks.xml

@@ -1,6 +1,6 @@
 <tool id="get_flanks1" name="Get flanks">
   <description>returns flanking region/s for every gene</description>
-  <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol</command>
+  <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Select data"/>
     <param name="region" type="select" label="Region">

tools/new_operations/intersect.xml

@@ -1,6 +1,6 @@
 <tool id="gops_intersect_1" name="Intersect">
   <description>the intervals of two queries</description>
-  <command interpreter="python">gops_intersect.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol -m $min $returntype</command>
+  <command interpreter="python">gops_intersect.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min $returntype</command>
   <inputs>
     <param name="returntype" type="select" label="Return" help="(see figure below)">
       <option value="">Overlapping Intervals</option>

tools/new_operations/join.xml

@@ -1,6 +1,6 @@
 <tool id="gops_join_1" name="Join">
   <description>the intervals of two queries side-by-side</description>
-  <command interpreter="python">gops_join.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol -m $min -f $fill</command>
+  <command interpreter="python">gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill</command>
   <inputs>
     <param format="interval" name="input1" type="data" help="First query">
       <label>Join</label>

tools/new_operations/merge.xml

@@ -1,6 +1,6 @@
 <tool id="gops_merge_1" name="Merge">
   <description>the overlapping intervals of a query</description>
-  <command interpreter="python">gops_merge.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol $returntype</command>
+  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
   <inputs>
     <param format="interval" name="input1" type="data">
       <label>Merge overlaping regions of</label>

tools/new_operations/subtract.xml

@@ -1,6 +1,6 @@
 <tool id="gops_subtract_1" name="Subtract">
   <description>the intervals of two queries</description>
-  <command interpreter="python">gops_subtract.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol -m $min $returntype</command>
+  <command interpreter="python">gops_subtract.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min $returntype</command>
   <inputs>
     <param format="interval" name="input2" type="data" help="Second query">
       <label>Subtract</label>

tools/regVariation/featureCounter.xml

@@ -1,6 +1,6 @@
 <tool id="featureCoverage1" name="Feature coverage" version="2.0.0">
   <description></description>
-  <command interpreter="python">featureCounter.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol</command>
+  <command interpreter="python">featureCounter.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command>
   <inputs>
     <param format="interval" name="input1" type="data" help="First query">
       <label>What portion of</label>

tools/regVariation/windowSplitter.xml

@@ -1,6 +1,6 @@
 <tool id="winSplitter" name="Make windows">
   <description></description>
-  <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol</command>
+  <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
   <inputs>
     <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
     <param format="interval" name="input" type="data" label="Select data"/>

tools/stats/aggregate_binned_scores_in_intervals.xml

@@ -1,8 +1,8 @@
 <tool id="aggregate_scores_in_intervals2" description="such as phastCons, GERP, binCons, and others for a set of genomic intervals" name="Aggregate datapoints" version="1.1.1">
   <description>Appends the average, min, max of datapoints per interval</description>
   <command interpreter="python">
-    #if $score_source_type.score_source == "user":#aggregate_scores_in_intervals.py $score_source_type.input2 $input1 $input1_chromCol $input1_startCol $input1_endCol $out_file1 --chrom_buffer=3
-    #else:#aggregate_scores_in_intervals.py $score_source_type.datasets $input1 $input1_chromCol $input1_startCol $input1_endCol $out_file1 -b
+    #if $score_source_type.score_source == "user":#aggregate_scores_in_intervals.py $score_source_type.input2 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 --chrom_buffer=3
+    #else:#aggregate_scores_in_intervals.py $score_source_type.datasets $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 -b
     #end if
   </command>
   <inputs>