From 5dd014a91e894132e6bab2298dca1570cf7d508b Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Wed, 23 Jul 2008 15:27:39 -0400 Subject: [PATCH] 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 | 14 ++++----- lib/galaxy/tools/__init__.py | 5 +--- lib/galaxy/tools/actions/__init__.py | 29 +++---------------- test/base/twilltestcase.py | 2 +- tool_conf.xml.main | 3 +- .../annotation_profiler.xml | 2 +- tools/encode/gencode_partition.xml | 2 +- tools/encode/random_intervals.xml | 5 ++-- tools/encode/split_by_partitions.py | 2 +- tools/extract/extract_genomic_dna.py | 2 +- tools/extract/extract_genomic_dna.xml | 2 +- tools/extract/phastOdds/phastOdds_tool.xml | 2 +- tools/maf/interval2maf.xml | 4 +-- tools/maf/interval2maf_pairwise.xml | 2 +- tools/maf/interval_maf_to_merged_fasta.xml | 4 +-- tools/maf/maf_stats.xml | 4 +-- tools/new_operations/basecoverage.xml | 2 +- tools/new_operations/cluster.xml | 2 +- tools/new_operations/complement.xml | 2 +- tools/new_operations/concat.xml | 2 +- tools/new_operations/coverage.xml | 2 +- tools/new_operations/flanking_features.xml | 2 +- tools/new_operations/get_flanks.xml | 2 +- tools/new_operations/intersect.xml | 2 +- tools/new_operations/join.xml | 2 +- tools/new_operations/merge.xml | 2 +- tools/new_operations/subtract.xml | 2 +- tools/regVariation/featureCounter.xml | 2 +- tools/regVariation/windowSplitter.xml | 2 +- .../aggregate_binned_scores_in_intervals.xml | 4 +-- 30 files changed, 44 insertions(+), 70 deletions(-) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index d6879e36e69..f673c7e519e 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/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 diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 2e3d3dda6b0..9a7f9a26781 100644 --- a/lib/galaxy/tools/__init__.py +++ b/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: diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index 595997b9719..f2bb0cd8185 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/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 diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 51cc2c57e49..29b0ff303a7 100644 --- a/test/base/twilltestcase.py +++ b/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" diff --git a/tool_conf.xml.main b/tool_conf.xml.main index 33021b0698e..ad26f1f0d65 100644 --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -85,9 +85,9 @@ +
@@ -107,6 +107,7 @@ +
diff --git a/tools/annotation_profiler/annotation_profiler.xml b/tools/annotation_profiler/annotation_profiler.xml index e297902ac63..a848feb8193 100644 --- a/tools/annotation_profiler/annotation_profiler.xml +++ b/tools/annotation_profiler/annotation_profiler.xml @@ -1,6 +1,6 @@ for a set of genomic intervals - 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 + 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 diff --git a/tools/encode/gencode_partition.xml b/tools/encode/gencode_partition.xml index a85282f49a3..415ae8a7b6c 100755 --- a/tools/encode/gencode_partition.xml +++ b/tools/encode/gencode_partition.xml @@ -1,6 +1,6 @@ an interval file - split_by_partitions.py /home/universe/encode_feature_partitions/partition_list.txt $input1 $out_file1 $input1_chromCol $input1_startCol $input1_endCol $input1_strandCol + 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} diff --git a/tools/encode/random_intervals.xml b/tools/encode/random_intervals.xml index f3a383b6bc8..a4846e0ff97 100644 --- a/tools/encode/random_intervals.xml +++ b/tools/encode/random_intervals.xml @@ -1,6 +1,6 @@ create a random set of intervals - 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} + 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} @@ -21,6 +21,7 @@ + @@ -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. ----- diff --git a/tools/encode/split_by_partitions.py b/tools/encode/split_by_partitions.py index 2e2a0065867..7bfd6650665 100755 --- a/tools/encode/split_by_partitions.py +++ b/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 diff --git a/tools/extract/extract_genomic_dna.py b/tools/extract/extract_genomic_dna.py index 6477c2f4d76..4bb2209dd96 100644 --- a/tools/extract/extract_genomic_dna.py +++ b/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 diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/extract_genomic_dna.xml index dad00536b53..f2deb9ef93a 100644 --- a/tools/extract/extract_genomic_dna.xml +++ b/tools/extract/extract_genomic_dna.xml @@ -1,6 +1,6 @@ using coordinates from assembled/unassembled genomes - extract_genomic_dna.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey $out_format ${GALAXY_DATA_INDEX_DIR} + 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} diff --git a/tools/extract/phastOdds/phastOdds_tool.xml b/tools/extract/phastOdds/phastOdds_tool.xml index 40e0de0a368..de290900668 100644 --- a/tools/extract/phastOdds/phastOdds_tool.xml +++ b/tools/extract/phastOdds/phastOdds_tool.xml @@ -1,6 +1,6 @@ for each interval - get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output $input_chromCol $input_startCol $input_endCol + get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} diff --git a/tools/maf/interval2maf.xml b/tools/maf/interval2maf.xml index a629d14b5aa..92816fc33cc 100644 --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -1,8 +1,8 @@ given a set of genomic intervals - #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=${GALAXY_DATA_INDEX_DIR}/maf_index.loc #end if diff --git a/tools/maf/interval2maf_pairwise.xml b/tools/maf/interval2maf_pairwise.xml index 5b00956afc6..a97401ae68f 100644 --- a/tools/maf/interval2maf_pairwise.xml +++ b/tools/maf/interval2maf_pairwise.xml @@ -1,6 +1,6 @@ given a set of genomic intervals - interval2maf.py --dbkey=$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 + 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 diff --git a/tools/maf/interval_maf_to_merged_fasta.xml b/tools/maf/interval_maf_to_merged_fasta.xml index 4d10bc5de52..698a7222e84 100644 --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -1,7 +1,7 @@ given a set of genomic intervals - #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} + #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 diff --git a/tools/maf/maf_stats.xml b/tools/maf/maf_stats.xml index 1fadd8176de..b86723f164c 100644 --- a/tools/maf/maf_stats.xml +++ b/tools/maf/maf_stats.xml @@ -3,9 +3,9 @@ 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} diff --git a/tools/new_operations/basecoverage.xml b/tools/new_operations/basecoverage.xml index 09bfb5221ee..91e68089097 100644 --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -1,6 +1,6 @@ of all intervals - gops_basecoverage.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol + gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} diff --git a/tools/new_operations/cluster.xml b/tools/new_operations/cluster.xml index 36d8ad53af1..a7a61d54ca6 100644 --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -1,6 +1,6 @@ the intervals of a query - gops_cluster.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -d $distance -m $minregions -o $returntype + gops_cluster.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -d $distance -m $minregions -o $returntype diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml index cccde19e0f6..84ca368c712 100644 --- a/tools/new_operations/complement.xml +++ b/tools/new_operations/complement.xml @@ -1,6 +1,6 @@ intervals of a query - 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 + 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 diff --git a/tools/new_operations/concat.xml b/tools/new_operations/concat.xml index 4c67358e85d..1996f516c7f 100644 --- a/tools/new_operations/concat.xml +++ b/tools/new_operations/concat.xml @@ -1,6 +1,6 @@ two queries into one query - 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 + 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 diff --git a/tools/new_operations/coverage.xml b/tools/new_operations/coverage.xml index 26a6d4bac35..63475e98fc5 100644 --- a/tools/new_operations/coverage.xml +++ b/tools/new_operations/coverage.xml @@ -1,6 +1,6 @@ of a set of intervals on second set of intervals - gops_coverage.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol + 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} diff --git a/tools/new_operations/flanking_features.xml b/tools/new_operations/flanking_features.xml index e1ff9b10231..1b05379b608 100644 --- a/tools/new_operations/flanking_features.xml +++ b/tools/new_operations/flanking_features.xml @@ -1,6 +1,6 @@ for every interval - 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 + 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} diff --git a/tools/new_operations/get_flanks.xml b/tools/new_operations/get_flanks.xml index bf92c259093..eb76d2d31c9 100644 --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -1,6 +1,6 @@ returns flanking region/s for every gene - get_flanks.py $input $out_file1 $size $direction $region -o $offset -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol + get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml index 68e8f18853a..17c297c942f 100644 --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -1,6 +1,6 @@ the intervals of two queries - 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 + 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 diff --git a/tools/new_operations/join.xml b/tools/new_operations/join.xml index 898c9292f64..082f392dd9a 100644 --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -1,6 +1,6 @@ the intervals of two queries side-by-side - 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 + 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 diff --git a/tools/new_operations/merge.xml b/tools/new_operations/merge.xml index 1f6be7eff43..ce7a349292c 100644 --- a/tools/new_operations/merge.xml +++ b/tools/new_operations/merge.xml @@ -1,6 +1,6 @@ the overlapping intervals of a query - gops_merge.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol $returntype + gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/subtract.xml index 60f3c155e9f..8d33b446312 100644 --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -1,6 +1,6 @@ the intervals of two queries - 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 + 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 diff --git a/tools/regVariation/featureCounter.xml b/tools/regVariation/featureCounter.xml index 73567baa301..d14f278bf1f 100644 --- a/tools/regVariation/featureCounter.xml +++ b/tools/regVariation/featureCounter.xml @@ -1,6 +1,6 @@ - featureCounter.py $input1 $input2 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -2 $input2_chromCol,$input2_startCol,$input2_endCol,$input2_strandCol + 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} diff --git a/tools/regVariation/windowSplitter.xml b/tools/regVariation/windowSplitter.xml index fd040b421fe..42f92fa5122 100644 --- a/tools/regVariation/windowSplitter.xml +++ b/tools/regVariation/windowSplitter.xml @@ -1,6 +1,6 @@ - windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol + windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} diff --git a/tools/stats/aggregate_binned_scores_in_intervals.xml b/tools/stats/aggregate_binned_scores_in_intervals.xml index 491cde1225d..d6f3f8bc847 100644 --- a/tools/stats/aggregate_binned_scores_in_intervals.xml +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml @@ -1,8 +1,8 @@ Appends the average, min, max of datapoints per interval - #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