mirror of
https://github.com/galaxyproject/galaxy.git
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Daniel Blankenberg
8bc14e03fa
'tool_conf.xml.main'. tool_conf.xml.sample is used by the Testing frame work to determine which tools to test, so it should have all tools undergoing testing.
368 lines
17 KiB
XML
368 lines
17 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_multiple_sets.xml" />
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<tool file="filters/maf/maf_to_fasta_concat.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/user_interval2maf.xml" />
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<tool file="extract/interval_maf_to_merged_fasta.xml" />
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<tool file="extract/interval_maf_to_merged_fasta_user.xml" />
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<!-- <tool file="extract/genebed_maf_to_fasta.xml"/>
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<tool file="extract/genebed_maf_to_fasta_user.xml"/>
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<tool file="filters/maf/maf_stats.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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</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="data_source/show_in_ucsc.xml" />
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<tool file="visualization/build_ucsc_custom_track.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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<!--
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<section name="Run EMBOSS nucleotide" id="EMBOSSnucleotide">
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<tool file="emboss/emboss_biosed.xml" />
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<tool file="emboss/emboss_btwisted.xml" />
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<tool file="emboss/emboss_cai.xml" />
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<tool file="emboss/emboss_chaos.xml" />
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<tool file="emboss/emboss_chips.xml" />
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<tool file="emboss/emboss_codcmp.xml" />
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<tool file="emboss/emboss_coderet.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_degapseq.xml" />
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<tool file="emboss/emboss_descseq.xml" />
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<tool file="emboss/emboss_diffseq.xml" />
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<tool file="emboss/emboss_dotmatcher.xml" />
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<tool file="emboss/emboss_dotpath.xml" />
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<tool file="emboss/emboss_dottup.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_extractfeat.xml" />
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<tool file="emboss/emboss_extractseq.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_geecee.xml" />
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<tool file="emboss/emboss_getorf.xml" />
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<tool file="emboss/emboss_helixturnhelix.xml" />
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<tool file="emboss/emboss_infoseq.xml" />
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<tool file="emboss/emboss_isochore.xml" />
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<tool file="emboss/emboss_marscan.xml" />
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<tool file="emboss/emboss_maskfeat.xml" />
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<tool file="emboss/emboss_maskseq.xml" />
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<tool file="emboss/emboss_matcher.xml" />
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<tool file="emboss/emboss_megamerger.xml" />
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<tool file="emboss/emboss_merger.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_noreturn.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_seqret.xml" />
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<tool file="emboss/emboss_showfeat.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_skipseq.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_stssearch.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_tcode.xml" />
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<tool file="emboss/emboss_textsearch.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_twofeat.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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</section>
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<section name="Run EMBOSS protein" id="EMBOSSprotein">
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<tool file="emboss/emboss_antigenic.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_chaos.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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<tool file="emboss/emboss_coderet.xml" />
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<tool file="emboss/emboss_compseq.xml" />
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<tool file="emboss/emboss_cutseq.xml" />
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<tool file="emboss/emboss_degapseq.xml" />
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<tool file="emboss/emboss_descseq.xml" />
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<tool file="emboss/emboss_diffseq.xml" />
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<tool file="emboss/emboss_digest.xml" />
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<tool file="emboss/emboss_dotmatcher.xml" />
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<tool file="emboss/emboss_dotpath.xml" />
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<tool file="emboss/emboss_dottup.xml" />
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<tool file="emboss/emboss_epestfind.xml" />
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<tool file="emboss/emboss_extractfeat.xml" />
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<tool file="emboss/emboss_extractseq.xml" />
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<tool file="emboss/emboss_freak.xml" />
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<tool file="emboss/emboss_fuzzpro.xml" />
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<tool file="emboss/emboss_garnier.xml" />
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<tool file="emboss/emboss_hmoment.xml" />
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<tool file="emboss/emboss_iep.xml" />
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<tool file="emboss/emboss_infoseq.xml" />
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<tool file="emboss/emboss_maskfeat.xml" />
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<tool file="emboss/emboss_maskseq.xml" />
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<tool file="emboss/emboss_matcher.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_newseq.xml" />
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<tool file="emboss/emboss_noreturn.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_octanol.xml" />
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<tool file="emboss/emboss_oddcomp.xml" />
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<tool file="emboss/emboss_pasteseq.xml" />
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<tool file="emboss/emboss_patmatdb.xml" />
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<tool file="emboss/emboss_pepcoil.xml" />
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<tool file="emboss/emboss_pepinfo.xml" />
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<tool file="emboss/emboss_pepstats.xml" />
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<tool file="emboss/emboss_pepwheel.xml" />
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<tool file="emboss/emboss_pepwindow.xml" />
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<tool file="emboss/emboss_pepwindowall.xml" />
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<tool file="emboss/emboss_polydot.xml" />
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<tool file="emboss/emboss_seqmatchall.xml" />
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<tool file="emboss/emboss_seqret.xml" />
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<tool file="emboss/emboss_showfeat.xml" />
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<tool file="emboss/emboss_shuffleseq.xml" />
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<tool file="emboss/emboss_sigcleave.xml" />
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<tool file="emboss/emboss_skipseq.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_textsearch.xml" />
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<tool file="emboss/emboss_tmap.xml" />
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<tool file="emboss/emboss_tranalign.xml" />
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<tool file="emboss/emboss_trimseq.xml" />
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<tool file="emboss/emboss_twofeat.xml" />
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<tool file="emboss/emboss_union.xml" />
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<tool file="emboss/emboss_water.xml" />
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<tool file="emboss/emboss_wordmatch.xml" />
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</section>
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-->
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<!--
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<section id="ePHYLIP" name="Run ePHYLIP">
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<tool file="emboss/phylip/emboss_eclique.xml" />
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<tool file="emboss/phylip/emboss_econsense.xml" />
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<tool file="emboss/phylip/emboss_econtml.xml" />
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<tool file="emboss/phylip/emboss_econtrast.xml" />
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<tool file="emboss/phylip/emboss_ednacomp.xml" />
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<tool file="emboss/phylip/emboss_ednadist.xml" />
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<tool file="emboss/phylip/emboss_ednainvar.xml" />
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<tool file="emboss/phylip/emboss_ednaml.xml" />
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<tool file="emboss/phylip/emboss_ednamlk.xml" />
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<tool file="emboss/phylip/emboss_ednapars.xml" />
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<tool file="emboss/phylip/emboss_ednapenny.xml" />
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<tool file="emboss/phylip/emboss_edollop.xml" />
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<tool file="emboss/phylip/emboss_edolpenny.xml" />
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<tool file="emboss/phylip/emboss_efactor.xml" />
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<tool file="emboss/phylip/emboss_efitch.xml" />
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<tool file="emboss/phylip/emboss_egendist.xml" />
|
|
<tool file="emboss/phylip/emboss_ekitsch.xml" />
|
|
<tool file="emboss/phylip/emboss_emix.xml" />
|
|
<tool file="emboss/phylip/emboss_eneighbor.xml" />
|
|
<tool file="emboss/phylip/emboss_epenny.xml" />
|
|
<tool file="emboss/phylip/emboss_eprotdist.xml" />
|
|
<tool file="emboss/phylip/emboss_eprotpars.xml" />
|
|
<tool file="emboss/phylip/emboss_erestml.xml" />
|
|
<tool file="emboss/phylip/emboss_eseqboot.xml" />
|
|
</section>
|
|
-->
|
|
<!-- <section name="PHYLIP" id="phylipnew">
|
|
<tool file="emboss/phylipnew/emboss_fdnadist.xml" />
|
|
<tool file="emboss/phylipnew/emboss_fdnapars.xml" />
|
|
<tool file="emboss/phylipnew/emboss_fdrawgram.xml" />
|
|
<tool file="emboss/phylipnew/emboss_ffitch.xml" />
|
|
<tool file="emboss/phylipnew/emboss_fseqboot.xml" />
|
|
<tool file="emboss/phylipnew/emboss_fneighbor.xml" />
|
|
<tool file="emboss/phylipnew/emboss_fprotdist.xml" />
|
|
<tool file="emboss/phylipnew/emboss_fprotpars.xml" />
|
|
</section> -->
|
|
<section name="HYPHY" id="hyphy">
|
|
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
|
|
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
|
|
</section>
|
|
</toolbox>
|