mirror of
https://github.com/galaxyproject/galaxy.git
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180 lines
8.0 KiB
XML
180 lines
8.0 KiB
XML
<?xml version="1.0"?>
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<toolbox>
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<section name="Get Data" id="getext">
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<tool file="data_source/upload.xml"/>
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<tool file="data_source/ucsc_tablebrowser.xml" />
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<tool file="data_source/ucsc_tablebrowser_test.xml" />
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<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
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<tool file="data_source/microbial_import.xml" />
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<tool file="data_source/biomart.xml" />
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<tool file="data_source/biomart_test.xml" />
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<tool file="data_source/encode_db.xml" />
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<tool file="data_source/hbvar.xml" />
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<tool file="validation/fix_errors.xml" />
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</section>
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<section name="Get ENCODE Data" id="encode">
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<tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/>
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<tool file="data_source/encode_import_genes_and_transcripts.xml"/>
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<tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/>
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<tool file="data_source/encode_import_transcription_regulation.xml"/>
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<tool file="data_source/encode_import_all_latest_datasets.xml" />
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<tool file="data_source/encode_import_gencode.xml" />
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</section>
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<section name="ENCODE Tools" id="EncodeTools">
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<!-- <tool file="extract/interval2maf.xml" />
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<tool file="extract/phastOdds/phastOdds_tool.xml" />
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<tool file="stats/aggregate_binned_scores_in_intervals.xml" /> -->
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<tool file="encode/gencode_partition.xml" />
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<tool file="encode/random_intervals.xml" />
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</section>
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<section name="Text Manipulation" id="textutil">
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<tool file="filters/fixedValueColumn.xml" />
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<tool file="stats/column_maker.xml" />
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<tool file="filters/catWrapper.xml" />
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<tool file="filters/condense_characters.xml" />
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<tool file="filters/convert_characters.xml" />
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<tool file="filters/CreateInterval.xml" />
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<tool file="filters/cutWrapper.xml" />
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<tool file="filters/pasteWrapper.xml" />
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<tool file="filters/remove_beginning.xml" />
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<tool file="filters/headWrapper.xml" />
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<tool file="filters/tailWrapper.xml" />
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</section>
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<section name="Filter and Sort" id="filter">
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<tool file="stats/filtering.xml" />
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<tool file="filters/sorter.xml" />
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<tool file="filters/grep.xml" />
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</section>
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<section name="Join, Subtract and Group" id="group">
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<tool file="filters/joiner.xml" />
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<tool file="filters/compare.xml"/>
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<tool file="new_operations/subtract_query.xml"/>
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<tool file="stats/grouping.xml" />
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</section>
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<section name="Convert Formats" id="convert">
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<tool file="filters/maf/maf_to_fasta.xml" />
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<tool file="filters/maf/maf_to_bed.xml" />
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<tool file="filters/gff2bed.xml" />
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<tool file="filters/bed2gff.xml" />
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<tool file="filters/axt_to_fasta.xml" />
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<tool file="filters/axt_to_concat_fasta.xml" />
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<tool file="filters/axt_to_lav.xml" />
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<tool file="filters/lav_to_bed.xml" />
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</section>
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<section name="Extract Features" id="features">
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<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
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<tool file="extract/extract_GFF_Features.xml" />
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</section>
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<section name="Pattern-Matching" id="patmat">
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<tool file="patmat/findcluster_mysql.xml" />
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</section>
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<section name="Fetch Sequences" id="fetchSeq">
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<tool file="extract/fasta-subseq-wrapper.xml" />
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<tool file="extract/twoBitToFa_wrapper.xml" />
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</section>
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<section name="Fetch Alignments" id="fetchAlign">
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<tool file="extract/interval2maf_pairwise.xml" />
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<tool file="extract/interval2maf.xml" />
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<tool file="extract/interval_maf_to_merged_fasta.xml" />
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<tool file="extract/genebed_maf_to_fasta.xml"/>
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<tool file="filters/maf/maf_stats.xml"/>
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<tool file="filters/maf/maf_thread_for_species.xml"/>
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<tool file="filters/maf/maf_limit_to_species.xml"/>
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<tool file="filters/maf/maf_limit_size.xml"/>
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<tool file="filters/maf/maf_by_block_number.xml"/>
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<tool file="filters/maf/maf_reverse_complement.xml"/>
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</section>
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<section name="Get Genomic Scores" id="scores">
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<tool file="stats/wiggle_to_simple.xml" />
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<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
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<tool file="extract/phastOdds/phastOdds_tool.xml" />
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</section>
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<section name="Operate on Genomic Intervals" id="bxops">
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<tool file="new_operations/intersect.xml" id="intersect" />
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<tool file="new_operations/subtract.xml" id="subtract" />
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<tool file="new_operations/merge.xml" id="merge" />
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<tool file="new_operations/concat.xml" id="concat" />
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<tool file="new_operations/basecoverage.xml" id="basecoverage" />
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<tool file="new_operations/coverage.xml" id="coverage" />
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<tool file="new_operations/complement.xml" id="complement" />
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<tool file="new_operations/cluster.xml" id="cluster" />
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<tool file="new_operations/join.xml" id="join" />
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<tool file="new_operations/get_flanks.xml" />
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</section>
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<section name="Statistics" id="stats">
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<tool file="stats/gsummary.xml" />
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<tool file="filters/uniq.xml" />
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<tool file="stats/cor.xml" />
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</section>
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<section name="Graph/Display Data" id="plots">
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<tool file="plotting/histogram2.xml" />
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<tool file="plotting/scatterplot.xml" />
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<tool file="plotting/xy_plot.xml" />
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<tool file="visualization/GMAJ.xml" />
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<tool file="visualization/LAJ.xml" />
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<tool file="visualization/build_ucsc_custom_track.xml" />
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</section>
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<section name="Evolution: HyPhy" id="hyphy">
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<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
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<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
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<tool file="hyphy/hyphy_dnds_wrapper.xml" />
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</section>
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<section name="EMBOSS" id="EMBOSSLite">
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<tool file="emboss/emboss_cai.xml" />
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<tool file="emboss/emboss_cai_custom.xml" />
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<!-- <tool file="emboss/emboss_codcmp.xml" /> -->
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<tool file="emboss/emboss_compseq.xml" />
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<!-- <tool file="emboss/emboss_cpgplot.xml" /> -->
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<tool file="emboss/emboss_cpgreport.xml" />
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<tool file="emboss/emboss_cusp.xml" />
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<tool file="emboss/emboss_cutseq.xml" />
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<!-- <tool file="emboss/emboss_dan.xml" /> -->
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<tool file="emboss/emboss_einverted.xml" />
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<tool file="emboss/emboss_equicktandem.xml" />
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<tool file="emboss/emboss_est2genome.xml" />
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<tool file="emboss/emboss_etandem.xml" />
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<!-- <tool file="emboss/emboss_freak.xml" /> -->
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<tool file="emboss/emboss_fuzznuc.xml" />
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<tool file="emboss/emboss_fuzztran.xml" />
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<tool file="emboss/emboss_getorf.xml" />
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<tool file="emboss/emboss_isochore.xml" />
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<tool file="emboss/emboss_msbar.xml" />
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<tool file="emboss/emboss_needle.xml" />
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<!-- <tool file="emboss/emboss_newcpgreport.xml" /> -->
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<tool file="emboss/emboss_newcpgseek.xml" />
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<tool file="emboss/emboss_newseq.xml" />
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<tool file="emboss/emboss_notseq.xml" />
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<tool file="emboss/emboss_nthseq.xml" />
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<tool file="emboss/emboss_palindrome.xml" />
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<tool file="emboss/emboss_pasteseq.xml" />
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<tool file="emboss/emboss_plotorf.xml" />
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<tool file="emboss/emboss_polydot.xml" />
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<tool file="emboss/emboss_prettyseq.xml" />
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<tool file="emboss/emboss_primersearch.xml" />
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<tool file="emboss/emboss_revseq.xml" />
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<tool file="emboss/emboss_seqmatchall.xml" />
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<!-- <tool file="emboss/emboss_showorf.xml" /> -->
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<tool file="emboss/emboss_shuffleseq.xml" />
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<tool file="emboss/emboss_sirna.xml" />
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<tool file="emboss/emboss_sixpack.xml" />
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<tool file="emboss/emboss_splitter.xml" />
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<!-- <tool file="emboss/emboss_stretcher.xml" /> -->
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<tool file="emboss/emboss_supermatcher.xml" />
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<tool file="emboss/emboss_syco.xml" />
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<tool file="emboss/emboss_tranalign.xml" />
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<tool file="emboss/emboss_transeq.xml" />
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<tool file="emboss/emboss_trimest.xml" />
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<tool file="emboss/emboss_trimseq.xml" />
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<tool file="emboss/emboss_union.xml" />
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<tool file="emboss/emboss_vectorstrip.xml" />
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<tool file="emboss/emboss_water.xml" />
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<tool file="emboss/emboss_wobble.xml" />
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<tool file="emboss/emboss_wordcount.xml" />
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<tool file="emboss/emboss_wordmatch.xml" />
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<tool file="emboss/emboss_backtranseq.xml" />
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<tool file="emboss/emboss_biosed.xml" />
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<tool file="emboss/emboss_charge.xml" />
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<tool file="emboss/emboss_checktrans.xml" />
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</section>
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</toolbox>
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