Changeset 1451:352694e163c7

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Timestamp:
07/23/08 15:27:39 (6 months ago)
Author:
greg
branch:
default
Message:

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}.

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  • lib/galaxy/jobs/__init__.py

    r1440 r1451  
    257257        # Do any validation that could not be done at job creation 
    258258        self.tool.handle_unvalidated_param_values( incoming, self.app ) 
    259         # Resore input / output data lists 
     259        # Restore input / output data lists 
    260260        inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) 
    261261        out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) 
    262         # add some useful session info to param_dict via incoming - ross august 2007 
    263         # these can be passed on the commandline if wanted as $userId $userEmail 
     262        # These can be passed on the command line if wanted as $userId $userEmail 
    264263        if job.history.user: # check for anonymous user! 
    265264             userId = '%d' % job.history.user.id 
    …… 
    272271        # Build params, done before hook so hook can use 
    273272        param_dict = self.tool.build_param_dict( incoming, inp_data, out_data ) 
    274         # Run the before queue ("exec_before_job") hook "trans" is no 
    275         # longer available to this hook, and has been replaced with 
    276         # app - 5/31/2007, by INS 
    277         # job added so we can get at the user if needed 14/august/2007 ross 
     273        # Run the before queue ("exec_before_job") hook 
    278274        self.tool.call_hook( 'exec_before_job', self.queue.app, inp_data=inp_data,  
    279275                             out_data=out_data, tool=self.tool, param_dict=incoming) 
    …… 
    288284        if self.command_line and self.command_line.startswith( 'python' ): 
    289285            self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root 
    290         # command_line won't actually be set in the db until finish unless you do it here 
    291         # We need it in the db to be able to restart jobs -ndc 
     286        # We need command_line persisted to the db in order for Galaxy to re-queue the job 
     287        # if the server was stopped and restarted before the job finished 
    292288        job.command_line = self.command_line 
    293289        job.flush() 

  • lib/galaxy/tools/__init__.py

    r1403 r1451  
    283283        # Parse tool help 
    284284        self.parse_help( root ) 
    285         # FIXME: This is not used anywhere, what does it do? 
    286         # url redirection to ougoings 
    287         self.redir_url  = root.find("url") 
    288285        # Description of outputs produced by an invocation of the tool 
    289286        self.outputs = {} 
    …… 
    10411038        try:                 
    10421039            # Substituting parameters into the command 
    1043             command_line = fill_template( self.command, context=param_dict )  
     1040            command_line = fill_template( self.command, context=param_dict ) 
    10441041            # Remove newlines from command line 
    10451042            command_line = command_line.replace( "\n", " " ).replace( "\r", " " ) 

  • lib/galaxy/tools/actions/__init__.py

    r1403 r1451  
    6565     
    6666    def execute(self, tool, trans, incoming={}, set_output_hid = True ): 
    67         out_data   = {} 
    68          
     67        out_data = {} 
    6968        # Collect any input datasets from the incoming parameters 
    7069        inp_data = self.collect_input_datasets( tool, incoming, trans ) 
    71          
    72         # Deal with input metadata, 'dbkey', names, and types 
    73          
    74         # FIXME: does this need to modify 'incoming' or should this be  
    75         #        moved into 'build_param_dict'? Is this just about getting the 
    76         #        metadata into the command line? 
    77         # NEED TO FIX THIS SOON. 
     70        # Deal with input dataset names, 'dbkey' and types 
    7871        input_names = [] 
    7972        input_ext = 'data' 
    8073        input_dbkey = incoming.get( "dbkey", "?" ) 
    81         input_meta = Bunch() 
    8274        for name, data in inp_data.items(): 
    8375            if data: 
    …… 
    8880            if data.dbkey not in [None, '?']: 
    8981                input_dbkey = data.dbkey 
    90             for meta_key, meta_value in data.metadata.items(): 
    91                 if meta_value is not None: 
    92                     meta_value = str(data.datatype.metadata_spec[meta_key].wrap(meta_value, data)) 
    93                     meta_key = '%s_%s' % (name, meta_key) 
    94                     incoming[meta_key] = meta_value 
    95                 else: 
    96                     incoming_key = '%s_%s' % (name, meta_key) 
    97                     incoming[incoming_key] = data.datatype.metadata_spec[meta_key].no_value 
    98  
    9982        # Build name for output datasets based on tool name and input names 
    10083        if len( input_names ) == 1: 
    …… 
    187170        job = trans.app.model.Job() 
    188171        job.session_id = trans.get_galaxy_session( create=True ).id 
    189         if trans.get_history() is not None: 
    190             job.history_id = trans.get_history().id 
     172        job.history_id = trans.history.id 
    191173        job.tool_id = tool.id 
    192174        try: 
    193             # For backward compatability, some tools may not have versions yet. 
     175            # For backward compatibility, some tools may not have versions yet. 
    194176            job.tool_version = tool.version 
    195177        except: 
    196178            job.tool_version = "1.0.0" 
    197         ## job.command_line = command_line 
    198         ## job.param_filename = param_filename 
    199179        # FIXME: Don't need all of incoming here, just the defined parameters 
    200180        #        from the tool. We need to deal with tools that pass all post 
    …… 
    213193        # Queue the job for execution 
    214194        trans.app.job_queue.put( job.id, tool ) 
    215         # IMPORTANT: keep the following event as is - we parse it for our session activity reports 
    216195        trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) 
    217196        return out_data 

  • test/base/twilltestcase.py

    r1157 r1451  
    217217    def _assert_dataset_state( self, elem, state ): 
    218218        if elem.get( 'state' ) != state: 
    219             errmsg = "Expecting dataset state '%s' but is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() ) 
     219            errmsg = "Expecting dataset state '%s', but state is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() ) 
    220220            errmsg += "---------------------- >> begin tool stderr << -----------------------\n" 
    221221            errmsg += self.get_job_stderr( elem.get( 'id' ) ) + "\n" 

  • tool_conf.xml.main

    r1279 r1451  
    8686    <tool file="maf/maf_limit_size.xml"/> 
    8787    <tool file="maf/maf_by_block_number.xml"/> 
     88    <tool file="maf/maf_filter.xml"/> 
    8889    <!--     
    8990    <tool file="maf/maf_reverse_complement.xml"/> 
    90     <tool file="maf/maf_filter.xml"/>  
    9191    --> 
    9292  </section> 
    …… 
    108108    <tool file="new_operations/get_flanks.xml" /> 
    109109    <tool file="new_operations/flanking_features.xml" /> 
     110    <tool file="annotation_profiler/annotation_profiler.xml" /> 
    110111  </section> 
    111112  <section name="Statistics" id="stats"> 

  • tools/annotation_profiler/annotation_profiler.xml

    r1353 r1451  
    11<tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0"> 
    22  <description>for a set of genomic intervals</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data" label="Choose Intervals"> 

  • tools/encode/gencode_partition.xml

    r1129 r1451  
    11<tool id="gencode_partition1" name="Gencode Partition"> 
    22  <description>an interval file</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param name="input1" type="data" format="interval" label="File to Partition"/> 

  • tools/encode/random_intervals.xml

    r1338 r1451  
    11<tool id="random_intervals1" name="Random Intervals"> 
    22<description>create a random set of intervals</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param name="input1" type="data" format="interval" label="File to Mimick"> 
    …… 
    2222        <column name="dbkey" index="0"/> 
    2323        <filter type="data_meta" ref="input1" key="dbkey" column="0" /> 
     24        <validator type="no_options" message="This tool currently only works with ENCODE data from genome builds hg16 or hg17."/> 
    2425      </options> 
    2526    </param>  
    …… 
    3233.. class:: warningmark 
    3334 
    34 This tool currently only works with data from genome builds hg16 or hg17. 
     35This tool currently only works with ENCODE data from genome builds hg16 or hg17. 
    3536 
    3637----- 

  • tools/encode/split_by_partitions.py

    r1172 r1451  
    5858        strandCol = int( sys.argv[7] )-1 
    5959    except: 
    60         stop_err( "Bad strand column: %s" % ( str( sys.argv[7] ) ) ) 
     60        strandCol = -1 
    6161     
    6262    line_count = 0 

  • tools/extract/extract_genomic_dna.py

    r1313 r1451  
    11#!/usr/bin/env python 
    22""" 
    3 usage: extract_genomic_dna.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey $out_format GALAXY_DATA_INDEX_DIR 
     3usage: 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 
    44by Wen-Yu Chung 
    55""" 

  • tools/extract/extract_genomic_dna.xml

    r1396 r1451  
    11<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.1.0"> 
    22  <description>using coordinates from assembled/unassembled genomes</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"> 

  • tools/extract/phastOdds/phastOdds_tool.xml

    r1338 r1451  
    11<tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0"> 
    22  <description>for each interval</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input" type="data" label="Interval file"> 

  • tools/maf/interval2maf.xml

    r1356 r1451  
    22  <description>given a set of genomic intervals</description> 
    33  <command interpreter="python"> 
    4     #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 
    5     #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 
     4    #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 
     5    #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 
    66    #end if 
    77  </command> 

  • tools/maf/interval2maf_pairwise.xml

    r1356 r1451  
    11<tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks"> 
    22  <description>given a set of genomic intervals</description> 
    3   <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=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command> 
     3  <command interpreter="python">interval2maf.py --dbkey=${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> 
    44  <inputs> 
    55    <param name="input1" type="data" format="interval" label="Interval File"> 

  • tools/maf/interval_maf_to_merged_fasta.xml

    r1356 r1451  
    11<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks"> 
    22  <description>given a set of genomic intervals</description> 
    3   <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} 
    4 #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} 
     3  <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} 
     4#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} 
    55#end if 
    66  </command> 

  • tools/maf/maf_stats.xml

    r1356 r1451  
    44    maf_stats.py 
    55    #if $maf_source_type.maf_source == "user": 
    6       $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol $summary 
     6      $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary 
    77    #else: 
    8       $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey $input1_chromCol $input1_startCol $input1_endCol $summary 
     8      $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary 
    99    #end if 
    1010    ${GALAXY_DATA_INDEX_DIR} 

  • tools/new_operations/basecoverage.xml

    r1323 r1451  
    11<tool id="gops_basecoverage_1" name="Base Coverage"> 
    22  <description>of all intervals</description> 
    3   <command interpreter="python">gops_basecoverage.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol</command> 
     3  <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data"> 

  • tools/new_operations/cluster.xml

    r1323 r1451  
    11<tool id="gops_cluster_1" name="Cluster"> 
    22  <description>the intervals of a query</description> 
    3   <command interpreter="python">gops_cluster.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol -d $distance -m $minregions -o $returntype</command> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data"> 

  • tools/new_operations/complement.xml

    r1353 r1451  
    11<tool id="gops_complement_1" name="Complement"> 
    22  <description>intervals of a query</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data"> 

  • tools/new_operations/concat.xml

    r1129 r1451  
    11<tool id="gops_concat_1" name="Concatenate"> 
    22  <description>two queries into one query</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data" help="First query"> 

  • tools/new_operations/coverage.xml

    r1323 r1451  
    11<tool id="gops_coverage_1" name="Coverage"> 
    22  <description>of a set of intervals on second set of intervals</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data" help="First query"> 

  • tools/new_operations/flanking_features.xml

    r1255 r1451  
    11<tool id="flanking_features_1" name="Fetch closest feature" version="2.0.0"> 
    22  <description>  for every interval</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data" label="For every interval in"/> 

  • tools/new_operations/get_flanks.xml

    r1129 r1451  
    11<tool id="get_flanks1" name="Get flanks"> 
    22  <description>returns flanking region/s for every gene</description> 
    3   <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol</command> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input" type="data" label="Select data"/> 

  • tools/new_operations/intersect.xml

    r1281 r1451  
    11<tool id="gops_intersect_1" name="Intersect"> 
    22  <description>the intervals of two queries</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param name="returntype" type="select" label="Return" help="(see figure below)"> 

  • tools/new_operations/join.xml

    r1129 r1451  
    11<tool id="gops_join_1" name="Join"> 
    22  <description>the intervals of two queries side-by-side</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data" help="First query"> 

  • tools/new_operations/merge.xml

    r1323 r1451  
    11<tool id="gops_merge_1" name="Merge"> 
    22  <description>the overlapping intervals of a query</description> 
    3   <command interpreter="python">gops_merge.py $input1 $output -1 $input1_chromCol,$input1_startCol,$input1_endCol,$input1_strandCol $returntype</command> 
     3  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data"> 

  • tools/new_operations/subtract.xml

    r1323 r1451  
    11<tool id="gops_subtract_1" name="Subtract"> 
    22  <description>the intervals of two queries</description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input2" type="data" help="Second query"> 

  • tools/regVariation/featureCounter.xml

    r1291 r1451  
    11<tool id="featureCoverage1" name="Feature coverage" version="2.0.0"> 
    22  <description></description> 
    3   <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> 
     3  <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> 
    44  <inputs> 
    55    <param format="interval" name="input1" type="data" help="First query"> 

  • tools/regVariation/windowSplitter.xml

    r1129 r1451  
    11<tool id="winSplitter" name="Make windows"> 
    22  <description></description> 
    3   <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol</command> 
     3  <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> 
    44  <inputs> 
    55    <!--<param label="Genome" name="dbkey" type="genomebuild"/>--> 

  • tools/stats/aggregate_binned_scores_in_intervals.xml

    r1356 r1451  
    22  <description>Appends the average, min, max of datapoints per interval</description> 
    33  <command interpreter="python"> 
    4     #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 
    5     #else:#aggregate_scores_in_intervals.py $score_source_type.datasets $input1 $input1_chromCol $input1_startCol $input1_endCol $out_file1 -b 
     4    #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 
     5    #else:#aggregate_scores_in_intervals.py $score_source_type.datasets $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $out_file1 -b 
    66    #end if 
    77  </command>