Changeset 1005:3ca890aafd79

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Timestamp:
02/27/08 19:08:05 (10 months ago)
Author:
Greg Von Kuster <greg@bx.psu.edu>
branch:
default
convert_revision:
svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2363
Message:

Restored version 1.1.0 of aggregate scores tool and moved the fixes to version 1.1.1.

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  • tool_conf.xml.main

    r990 r1005  
    6666  --> 
    6767  <section name="Fetch Sequences" id="fetchSeq"> 
    68     <!--  
    69     These are deprecated 
    70     <tool file="extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml" /> 
    71     <tool file="extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml" /> 
    72     --> 
    7368    <tool file="extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml" /> 
    7469  </section> 
    …… 
    9085  <section name="Get Genomic Scores" id="scores"> 
    9186    <tool file="stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml" /> 
    92     <tool file="stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml" /> 
     87    <tool file="stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml" /> 
    9388    <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" /> 
    9489  </section> 
    …… 
    132127    <tool file="hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml" /> 
    133128 </section> 
    134  <!-- 
    135  These are deprecated 
    136  <section name="EMBOSS" id="EMBOSSLite"> 
    137     <tool file="emboss/emboss_cai.xml" /> 
    138     <tool file="emboss/emboss_cai_custom.xml" /> 
    139     <tool file="emboss/emboss_codcmp.xml" /> 
    140     <tool file="emboss/emboss_compseq.xml" /> 
    141     <tool file="emboss/emboss_cpgplot.xml" /> 
    142     <tool file="emboss/emboss_cpgreport.xml" /> 
    143     <tool file="emboss/emboss_cusp.xml" /> 
    144     <tool file="emboss/emboss_cutseq.xml" /> 
    145     <tool file="emboss/emboss_dan.xml" /> 
    146     <tool file="emboss/emboss_einverted.xml" /> 
    147     <tool file="emboss/emboss_equicktandem.xml" /> 
    148     <tool file="emboss/emboss_est2genome.xml" /> 
    149     <tool file="emboss/emboss_etandem.xml" /> 
    150     <tool file="emboss/emboss_freak.xml" /> 
    151     <tool file="emboss/emboss_fuzznuc.xml" /> 
    152     <tool file="emboss/emboss_fuzztran.xml" /> 
    153     <tool file="emboss/emboss_getorf.xml" /> 
    154     <tool file="emboss/emboss_isochore.xml" /> 
    155     <tool file="emboss/emboss_msbar.xml" /> 
    156     <tool file="emboss/emboss_needle.xml" /> 
    157     <tool file="emboss/emboss_newcpgreport.xml" /> 
    158     <tool file="emboss/emboss_newcpgseek.xml" /> 
    159     <tool file="emboss/emboss_newseq.xml" /> 
    160     <tool file="emboss/emboss_notseq.xml" /> 
    161     <tool file="emboss/emboss_nthseq.xml" /> 
    162     <tool file="emboss/emboss_palindrome.xml" /> 
    163     <tool file="emboss/emboss_pasteseq.xml" /> 
    164     <tool file="emboss/emboss_plotorf.xml" /> 
    165     <tool file="emboss/emboss_polydot.xml" /> 
    166     <tool file="emboss/emboss_prettyseq.xml" /> 
    167     <tool file="emboss/emboss_primersearch.xml" /> 
    168     <tool file="emboss/emboss_revseq.xml" /> 
    169     <tool file="emboss/emboss_seqmatchall.xml" /> 
    170     <tool file="emboss/emboss_showorf.xml" /> 
    171     <tool file="emboss/emboss_shuffleseq.xml" /> 
    172     <tool file="emboss/emboss_sirna.xml" /> 
    173     <tool file="emboss/emboss_sixpack.xml" /> 
    174     <tool file="emboss/emboss_splitter.xml" /> 
    175     <tool file="emboss/emboss_stretcher.xml" /> 
    176     <tool file="emboss/emboss_supermatcher.xml" /> 
    177     <tool file="emboss/emboss_syco.xml" /> 
    178     <tool file="emboss/emboss_tranalign.xml" /> 
    179     <tool file="emboss/emboss_transeq.xml" /> 
    180     <tool file="emboss/emboss_trimest.xml" /> 
    181     <tool file="emboss/emboss_trimseq.xml" /> 
    182     <tool file="emboss/emboss_union.xml" /> 
    183     <tool file="emboss/emboss_vectorstrip.xml" /> 
    184     <tool file="emboss/emboss_water.xml" /> 
    185     <tool file="emboss/emboss_wobble.xml" /> 
    186     <tool file="emboss/emboss_wordcount.xml" /> 
    187     <tool file="emboss/emboss_wordmatch.xml" /> 
    188     <tool file="emboss/emboss_backtranseq.xml" /> 
    189     <tool file="emboss/emboss_biosed.xml" /> 
    190     <tool file="emboss/emboss_charge.xml" /> 
    191     <tool file="emboss/emboss_checktrans.xml" /> 
    192   </section> 
    193   --> 
    194129  <section name="EMBOSS" id="EMBOSSLite"> 
    195130    <tool file="emboss_5/emboss_antigenic.xml" /> 

  • tool_conf.xml.sample

    r995 r1005  
    7373  </section> 
    7474  <section name="Fetch Sequences" id="fetchSeq"> 
    75     <!--  
    76     These are deprecated 
    77     <tool file="extract/Extract_genomic_DNA_1/1.0.0/fasta-subseq-wrapper.xml" /> 
    78     <tool file="extract/Extract_genomic_DNA_1/1.0.0/twoBitToFa_wrapper.xml" /> 
    79     --> 
    8075    <tool file="extract/Extract_genomic_DNA_1/2.0.0/extract_genomic_dna.xml" /> 
    8176  </section> 
    …… 
    9590  <section name="Get Genomic Scores" id="scores"> 
    9691    <tool file="stats/wiggle2simple1/1.0.0/wiggle_to_simple.xml" /> 
    97     <tool file="stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml" /> 
     92    <tool file="stats/aggregate_scores_in_intervals2/1.1.1/aggregate_binned_scores_in_intervals.xml" /> 
    9893    <tool file="extract/phastOdds/phastOdds_for_intervals/1.0.0/phastOdds_tool.xml" /> 
    9994  </section> 
    …… 
    136131    <tool file="hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml" /> 
    137132 </section> 
    138  <!-- 
    139  These are deprecated 
    140  <section name="EMBOSS" id="EMBOSSLite"> 
    141     <tool file="emboss/emboss_cai.xml" /> 
    142     <tool file="emboss/emboss_cai_custom.xml" /> 
    143     <tool file="emboss/emboss_codcmp.xml" /> 
    144     <tool file="emboss/emboss_compseq.xml" /> 
    145     <tool file="emboss/emboss_cpgplot.xml" /> 
    146     <tool file="emboss/emboss_cpgreport.xml" /> 
    147     <tool file="emboss/emboss_cusp.xml" /> 
    148     <tool file="emboss/emboss_cutseq.xml" /> 
    149     <tool file="emboss/emboss_dan.xml" /> 
    150     <tool file="emboss/emboss_einverted.xml" /> 
    151     <tool file="emboss/emboss_equicktandem.xml" /> 
    152     <tool file="emboss/emboss_est2genome.xml" /> 
    153     <tool file="emboss/emboss_etandem.xml" /> 
    154     <tool file="emboss/emboss_freak.xml" /> 
    155     <tool file="emboss/emboss_fuzznuc.xml" /> 
    156     <tool file="emboss/emboss_fuzztran.xml" /> 
    157     <tool file="emboss/emboss_getorf.xml" /> 
    158     <tool file="emboss/emboss_isochore.xml" /> 
    159     <tool file="emboss/emboss_msbar.xml" /> 
    160     <tool file="emboss/emboss_needle.xml" /> 
    161     <tool file="emboss/emboss_newcpgreport.xml" /> 
    162     <tool file="emboss/emboss_newcpgseek.xml" /> 
    163     <tool file="emboss/emboss_newseq.xml" /> 
    164     <tool file="emboss/emboss_notseq.xml" /> 
    165     <tool file="emboss/emboss_nthseq.xml" /> 
    166     <tool file="emboss/emboss_palindrome.xml" /> 
    167     <tool file="emboss/emboss_pasteseq.xml" /> 
    168     <tool file="emboss/emboss_plotorf.xml" /> 
    169     <tool file="emboss/emboss_polydot.xml" /> 
    170     <tool file="emboss/emboss_prettyseq.xml" /> 
    171     <tool file="emboss/emboss_primersearch.xml" /> 
    172     <tool file="emboss/emboss_revseq.xml" /> 
    173     <tool file="emboss/emboss_seqmatchall.xml" /> 
    174     <tool file="emboss/emboss_showorf.xml" /> 
    175     <tool file="emboss/emboss_shuffleseq.xml" /> 
    176     <tool file="emboss/emboss_sirna.xml" /> 
    177     <tool file="emboss/emboss_sixpack.xml" /> 
    178     <tool file="emboss/emboss_splitter.xml" /> 
    179     <tool file="emboss/emboss_stretcher.xml" /> 
    180     <tool file="emboss/emboss_supermatcher.xml" /> 
    181     <tool file="emboss/emboss_syco.xml" /> 
    182     <tool file="emboss/emboss_tranalign.xml" /> 
    183     <tool file="emboss/emboss_transeq.xml" /> 
    184     <tool file="emboss/emboss_trimest.xml" /> 
    185     <tool file="emboss/emboss_trimseq.xml" /> 
    186     <tool file="emboss/emboss_union.xml" /> 
    187     <tool file="emboss/emboss_vectorstrip.xml" /> 
    188     <tool file="emboss/emboss_water.xml" /> 
    189     <tool file="emboss/emboss_wobble.xml" /> 
    190     <tool file="emboss/emboss_wordcount.xml" /> 
    191     <tool file="emboss/emboss_wordmatch.xml" /> 
    192     <tool file="emboss/emboss_backtranseq.xml" /> 
    193     <tool file="emboss/emboss_biosed.xml" /> 
    194     <tool file="emboss/emboss_charge.xml" /> 
    195     <tool file="emboss/emboss_checktrans.xml" /> 
    196   </section> 
    197   --> 
    198133  <!-- 
    199134  TODO: uncomment the following EMBOSS section whenever  

  • tools/stats/aggregate_scores_in_intervals2/1.1.0/aggregate_binned_scores_in_intervals.xml

    r1004 r1005  
    77  </command> 
    88  <inputs> 
    9     <param format="interval" name="input1" type="data" label="Interval file"> 
    10       <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/> 
    11     </param> 
     9    <param format="interval" name="input1" type="data" label="Interval file"/> 
    1210    <conditional name="score_source_type"> 
    1311      <param name="score_source" type="select" label="Score Source"> 

  • tools/stats/aggregate_scores_in_intervals2/1.1.0/aggregate_scores_in_intervals.py

    r1003 r1005  
    6363            if chrom not in scores_by_chrom: 
    6464                scores_by_chrom[chrom] = BinnedArray() 
    65             scores_by_chrom[chrom][pos] = val 
     65                scores_by_chrom[chrom][pos] = val 
    6666    except UCSCLimitException: 
    6767        # Wiggle data was truncated, at the very least need to warn the user.