/
tool_conf.xml
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/
tool_conf.xml
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<?xml version='1.0'?>
<toolbox>
<section name='Get Data' id='getext'>
<tool file='data_source/upload.xml'/>
<tool file='data_source/access_libraries.xml'/>
<tool file='data_source/ucsc_tablebrowser.xml'/>
<tool file='data_source/ucsc_tablebrowser_test.xml'/>
<tool file='data_source/ucsc_tablebrowser_archaea.xml'/>
<tool file='data_source/microbial_import.xml'/>
<tool file='data_source/biomart.xml'/>
<tool file='data_source/biomart_test.xml'/>
<tool file='data_source/gbrowse_elegans.xml'/>
<tool file='data_source/flymine.xml'/>
<tool file='data_source/encode_db.xml'/>
<tool file='data_source/epigraph_import.xml'/>
<tool file='data_source/epigraph_import_test.xml'/>
<tool file='data_source/hbvar.xml'/>
<tool file='validation/fix_errors.xml'/>
</section>
<section name='Get ENCODE Data' id='encode'>
<tool file='data_source/encode_import_chromatin_and_chromosomes.xml'/>
<tool file='data_source/encode_import_genes_and_transcripts.xml'/>
<tool file='data_source/encode_import_multi-species_sequence_analysis.xml'/>
<tool file='data_source/encode_import_transcription_regulation.xml'/>
<tool file='data_source/encode_import_all_latest_datasets.xml'/>
<tool file='data_source/encode_import_gencode.xml'/>
</section>
<section name='Send Data' id='send'>
<tool file='data_destination/epigraph.xml'/>
<tool file='data_destination/epigraph_test.xml'/>
</section>
<section name='ENCODE Tools' id='EncodeTools'>
<tool file='encode/gencode_partition.xml'/>
<tool file='encode/random_intervals.xml'/>
</section>
<section name='Lift-Over' id='liftOver'>
<tool file='extract/liftOver_wrapper.xml'/>
</section>
<section name='Text Manipulation' id='textutil'>
<tool file='filters/fixedValueColumn.xml'/>
<tool file='stats/column_maker.xml'/>
<tool file='filters/catWrapper.xml'/>
<tool file='filters/condense_characters.xml'/>
<tool file='filters/convert_characters.xml'/>
<tool file='filters/CreateInterval.xml'/>
<tool file='filters/cutWrapper.xml'/>
<tool file='filters/changeCase.xml'/>
<tool file='filters/pasteWrapper.xml'/>
<tool file='filters/remove_beginning.xml'/>
<tool file='filters/headWrapper.xml'/>
<tool file='filters/tailWrapper.xml'/>
</section>
<section name='Filter and Sort' id='filter'>
<tool file='stats/filtering.xml'/>
<tool file='filters/sorter.xml'/>
<tool file='filters/grep.xml'/>
</section>
<section name='Join, Subtract and Group' id='group'>
<tool file='filters/joiner.xml'/>
<tool file='filters/compare.xml'/>
<tool file='new_operations/subtract_query.xml'/>
<tool file='stats/grouping.xml'/>
</section>
<section name='Convert Formats' id='convert'>
<tool file='filters/axt_to_concat_fasta.xml'/>
<tool file='filters/axt_to_fasta.xml'/>
<tool file='filters/axt_to_lav.xml'/>
<tool file='filters/bed2gff.xml'/>
<tool file='fasta_tools/fasta_to_tabular.xml'/>
<tool file='metag_tools/fastqsolexa_to_fasta_qual.xml'/>
<tool file='filters/gff2bed.xml'/>
<tool file='filters/lav_to_bed.xml'/>
<tool file='maf/maf_to_bed.xml'/>
<tool file='maf/maf_to_fasta.xml'/>
<tool file='fasta_tools/tabular_to_fasta.xml'/>
</section>
<section name='Extract Features' id='features'>
<tool file='filters/ucsc_gene_bed_to_exon_bed.xml'/>
<tool file='extract/extract_GFF_Features.xml'/>
</section>
<section name='Fetch Sequences' id='fetchSeq'>
<tool file='extract/extract_genomic_dna.xml'/>
</section>
<section name='Fetch Alignments' id='fetchAlign'>
<tool file='maf/interval2maf_pairwise.xml'/>
<tool file='maf/interval2maf.xml'/>
<tool file='maf/interval_maf_to_merged_fasta.xml'/>
<tool file='maf/genebed_maf_to_fasta.xml'/>
<tool file='maf/maf_stats.xml'/>
<tool file='maf/maf_thread_for_species.xml'/>
<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_reverse_complement.xml'/>
<tool file='maf/maf_filter.xml'/>
</section>
<section name='Get Genomic Scores' id='scores'>
<tool file='stats/wiggle_to_simple.xml'/>
<tool file='stats/aggregate_binned_scores_in_intervals.xml'/>
<tool file='extract/phastOdds/phastOdds_tool.xml'/>
</section>
<section name='Operate on Genomic Intervals' id='bxops'>
<tool file='new_operations/intersect.xml'/>
<tool file='new_operations/subtract.xml'/>
<tool file='new_operations/merge.xml'/>
<tool file='new_operations/concat.xml'/>
<tool file='new_operations/basecoverage.xml'/>
<tool file='new_operations/coverage.xml'/>
<tool file='new_operations/complement.xml'/>
<tool id='cluster' file='new_operations/cluster.xml'/>
<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'/>
<tool file='filters/uniq.xml'/>
<tool file='stats/cor.xml'/>
</section>
<section name='Graph/Display Data' id='plots'>
<tool file='plotting/histogram2.xml'/>
<tool file='plotting/scatterplot.xml'/>
<tool file='plotting/bar_chart.xml'/>
<tool file='plotting/xy_plot.xml'/>
<tool file='visualization/GMAJ.xml'/>
<tool file='visualization/LAJ.xml'/>
<tool file='visualization/build_ucsc_custom_track.xml'/>
</section>
<section name='Regional Variation' id='regVar'>
<tool file='regVariation/windowSplitter.xml'/>
<tool file='regVariation/featureCounter.xml'/>
<tool file='regVariation/quality_filter.xml'/>
<tool file='regVariation/maf_cpg_filter.xml'/>
<tool file='regVariation/getIndels_2way.xml'/>
<tool file='regVariation/getIndels_3way.xml'/>
<tool file='regVariation/getIndelRates_3way.xml'/>
<tool file='regVariation/substitutions.xml'/>
<tool file='regVariation/substitution_rates.xml'/>
<tool file='regVariation/microsats_alignment_level.xml'/>
<tool file='regVariation/microsats_mutability.xml'/>
</section>
<section name='Multiple regression' id='multReg'>
<tool file='regVariation/linear_regression.xml'/>
<tool file='regVariation/best_regression_subsets.xml'/>
<tool file='regVariation/rcve.xml'/>
</section>
<section name='Evolution: HyPhy' id='hyphy'>
<tool file='hyphy/hyphy_branch_lengths_wrapper.xml'/>
<tool file='hyphy/hyphy_nj_tree_wrapper.xml'/>
<tool file='hyphy/hyphy_dnds_wrapper.xml'/>
</section>
<section name='Taxonomy manipulation' id='tax_manipulation'>
<tool file='taxonomy/gi2taxonomy.xml'/>
<tool file='taxonomy/t2t_report.xml'/>
<tool file='taxonomy/t2ps_wrapper.xml'/>
<tool file='taxonomy/find_diag_hits.xml'/>
<tool file='taxonomy/poisson2test.xml'/>
</section>
<section name='Solexa tools' id='solexa_tools'>
<tool file='sr_mapping/fastq_statistics.xml'/>
<tool file='sr_mapping/lastz_wrapper.xml'/>
</section>
<!--
TODO: uncomment the following EMBOSS section whenever
moving to test, but comment it in .sample to eliminate
it from buildbot functional tests since these tools
rarely change.
-->
<section name='EMBOSS' id='EMBOSSLite'>
<tool file='emboss_5/emboss_antigenic.xml'/>
<tool file='emboss_5/emboss_backtranseq.xml'/>
<tool file='emboss_5/emboss_banana.xml'/>
<tool file='emboss_5/emboss_biosed.xml'/>
<tool file='emboss_5/emboss_btwisted.xml'/>
<tool file='emboss_5/emboss_cai_custom.xml'/>
<tool file='emboss_5/emboss_cai.xml'/>
<tool file='emboss_5/emboss_chaos.xml'/>
<tool file='emboss_5/emboss_charge.xml'/>
<tool file='emboss_5/emboss_checktrans.xml'/>
<tool file='emboss_5/emboss_chips.xml'/>
<tool file='emboss_5/emboss_cirdna.xml'/>
<tool file='emboss_5/emboss_codcmp.xml'/>
<tool file='emboss_5/emboss_coderet.xml'/>
<tool file='emboss_5/emboss_compseq.xml'/>
<tool file='emboss_5/emboss_cpgplot.xml'/>
<tool file='emboss_5/emboss_cpgreport.xml'/>
<tool file='emboss_5/emboss_cusp.xml'/>
<tool file='emboss_5/emboss_cutseq.xml'/>
<tool file='emboss_5/emboss_dan.xml'/>
<tool file='emboss_5/emboss_degapseq.xml'/>
<tool file='emboss_5/emboss_descseq.xml'/>
<tool file='emboss_5/emboss_diffseq.xml'/>
<tool file='emboss_5/emboss_digest.xml'/>
<tool file='emboss_5/emboss_dotmatcher.xml'/>
<tool file='emboss_5/emboss_dotpath.xml'/>
<tool file='emboss_5/emboss_dottup.xml'/>
<tool file='emboss_5/emboss_dreg.xml'/>
<tool file='emboss_5/emboss_einverted.xml'/>
<tool file='emboss_5/emboss_epestfind.xml'/>
<tool file='emboss_5/emboss_equicktandem.xml'/>
<tool file='emboss_5/emboss_est2genome.xml'/>
<tool file='emboss_5/emboss_etandem.xml'/>
<tool file='emboss_5/emboss_extractfeat.xml'/>
<tool file='emboss_5/emboss_extractseq.xml'/>
<tool file='emboss_5/emboss_freak.xml'/>
<tool file='emboss_5/emboss_fuzznuc.xml'/>
<tool file='emboss_5/emboss_fuzzpro.xml'/>
<tool file='emboss_5/emboss_fuzztran.xml'/>
<tool file='emboss_5/emboss_garnier.xml'/>
<tool file='emboss_5/emboss_geecee.xml'/>
<tool file='emboss_5/emboss_getorf.xml'/>
<tool file='emboss_5/emboss_helixturnhelix.xml'/>
<tool file='emboss_5/emboss_hmoment.xml'/>
<tool file='emboss_5/emboss_iep.xml'/>
<tool file='emboss_5/emboss_infoseq.xml'/>
<tool file='emboss_5/emboss_isochore.xml'/>
<tool file='emboss_5/emboss_lindna.xml'/>
<tool file='emboss_5/emboss_marscan.xml'/>
<tool file='emboss_5/emboss_maskfeat.xml'/>
<tool file='emboss_5/emboss_maskseq.xml'/>
<tool file='emboss_5/emboss_matcher.xml'/>
<tool file='emboss_5/emboss_megamerger.xml'/>
<tool file='emboss_5/emboss_merger.xml'/>
<tool file='emboss_5/emboss_msbar.xml'/>
<tool file='emboss_5/emboss_needle.xml'/>
<tool file='emboss_5/emboss_newcpgreport.xml'/>
<tool file='emboss_5/emboss_newcpgseek.xml'/>
<tool file='emboss_5/emboss_newseq.xml'/>
<tool file='emboss_5/emboss_noreturn.xml'/>
<tool file='emboss_5/emboss_notseq.xml'/>
<tool file='emboss_5/emboss_nthseq.xml'/>
<tool file='emboss_5/emboss_octanol.xml'/>
<tool file='emboss_5/emboss_oddcomp.xml'/>
<tool file='emboss_5/emboss_palindrome.xml'/>
<tool file='emboss_5/emboss_pasteseq.xml'/>
<tool file='emboss_5/emboss_patmatdb.xml'/>
<tool file='emboss_5/emboss_pepcoil.xml'/>
<tool file='emboss_5/emboss_pepinfo.xml'/>
<tool file='emboss_5/emboss_pepnet.xml'/>
<tool file='emboss_5/emboss_pepstats.xml'/>
<tool file='emboss_5/emboss_pepwheel.xml'/>
<tool file='emboss_5/emboss_pepwindow.xml'/>
<tool file='emboss_5/emboss_pepwindowall.xml'/>
<tool file='emboss_5/emboss_plotcon.xml'/>
<tool file='emboss_5/emboss_plotorf.xml'/>
<tool file='emboss_5/emboss_polydot.xml'/>
<tool file='emboss_5/emboss_preg.xml'/>
<tool file='emboss_5/emboss_prettyplot.xml'/>
<tool file='emboss_5/emboss_prettyseq.xml'/>
<tool file='emboss_5/emboss_primersearch.xml'/>
<tool file='emboss_5/emboss_revseq.xml'/>
<tool file='emboss_5/emboss_seqmatchall.xml'/>
<tool file='emboss_5/emboss_seqret.xml'/>
<tool file='emboss_5/emboss_showfeat.xml'/>
<tool file='emboss_5/emboss_shuffleseq.xml'/>
<tool file='emboss_5/emboss_sigcleave.xml'/>
<tool file='emboss_5/emboss_sirna.xml'/>
<tool file='emboss_5/emboss_sixpack.xml'/>
<tool file='emboss_5/emboss_skipseq.xml'/>
<tool file='emboss_5/emboss_splitter.xml'/>
<tool file='emboss_5/emboss_supermatcher.xml'/>
<tool file='emboss_5/emboss_syco.xml'/>
<tool file='emboss_5/emboss_tcode.xml'/>
<tool file='emboss_5/emboss_textsearch.xml'/>
<tool file='emboss_5/emboss_tmap.xml'/>
<tool file='emboss_5/emboss_tranalign.xml'/>
<tool file='emboss_5/emboss_transeq.xml'/>
<tool file='emboss_5/emboss_trimest.xml'/>
<tool file='emboss_5/emboss_trimseq.xml'/>
<tool file='emboss_5/emboss_twofeat.xml'/>
<tool file='emboss_5/emboss_union.xml'/>
<tool file='emboss_5/emboss_vectorstrip.xml'/>
<tool file='emboss_5/emboss_water.xml'/>
<tool file='emboss_5/emboss_wobble.xml'/>
<tool file='emboss_5/emboss_wordcount.xml'/>
<tool file='emboss_5/emboss_wordmatch.xml'/>
</section>
<section name='FASTA manipulation' id='fasta_manipulation'>
<tool file='fasta_tools/fasta_compute_length.xml'/>
<tool file='fasta_tools/fasta_filter_by_length.xml'/>
<tool file='fasta_tools/fasta_concatenate_by_species.xml'/>
<tool file='fasta_tools/fasta_to_tabular.xml'/>
<tool file='fasta_tools/tabular_to_fasta.xml'/>
</section>
<section name='Short Read QC and Manipulation' id='short_read_analysis'>
<tool file='metag_tools/short_reads_figure_score.xml'/>
<tool file='metag_tools/short_reads_figure_high_quality_length.xml'/>
<tool file='metag_tools/short_reads_trim_seq.xml'/>
<tool file='metag_tools/blat_coverage_report.xml'/>
<tool file='metag_tools/split_paired_reads.xml'/>
</section>
<section name='Short Read Mapping' id='solexa_tools'>
<tool file='metag_tools/shrimp_color_wrapper.xml'/>
<tool file='metag_tools/shrimp_wrapper.xml'/>
<tool file='sr_mapping/lastz_wrapper.xml'/>
<tool file='metag_tools/megablast_wrapper.xml'/>
<tool file='metag_tools/megablast_xml_parser.xml'/>
<tool file='metag_tools/blat_wrapper.xml'/>
<tool file='metag_tools/mapping_to_ucsc.xml'/>
</section>
<section name='TogoWS' id='togows'>
<tool file='togows/search_resources.xml'/>
<tool file='togows/search_resources_with_history.xml'/>
<tool file='togows/get_restful_resources.xml'/>
</section>
<section name='Text Mining Tools' id='tmtools'>
<tool file='tmtools/related_pne_articles.xml'/>
<tool file='tmtools/pne_search.xml'/>
<tool file='tmtools/load_requested_medline_abstract.xml'/>
<tool file='tmtools/load_ner_results.xml'/>
<tool file='tmtools/medline_search_with_biomedical_ner.xml'/>
<tool file='tmtools/orefil_search.xml'/>
<tool file='tmtools/orefil_search_with_history.xml'/>
</section>
<section name='MEDLINE search' id='medline'>
<tool file='medline/search_medline_direct.xml'/>
<tool file='medline/search_medline_with_history.xml'/>
</section>
<section name='Experimental Tools' id='experimental'>
<tool file='experimental/rss.xml'/>
<tool file='experimental/link.xml'/>
<tool file='experimental/pfam_location.xml'/>
<tool file='experimental/pdbj_location.xml'/>
<tool file='experimental/external_form_orefil_search.xml'/>
</section>
<section name='Data Viewer' id='bookmarklet'>
<tool file='togows/bookmarklets.xml'/>
</section>
<section name='Pubmed' id='pubmed'>
<tool file='pubmed/pubmed_get_resource.xml'/>
</section>
</toolbox>