mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Daniel Blankenberg
74784e1755
Biomart doesn't work on the trunk yet (Before or after this commit). axt to lav tool won't be functional until multiple datasets per history item is available on trunk - although I could make it so that only the lav file is generated and no fasta files, in which case it wouldn't be an issue.
360 lines
16 KiB
XML
360 lines
16 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_proxy.xml"/>
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<tool file="data_source/ucsc_testproxy.xml" />
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<tool file="data_source/ucsc_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/encode_db.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="Edit Queries" id="textutil">
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<tool file="filters/fixedValueColumn.xml" />
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<!-- <tool file="operations/combineLists.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, Sort, Join and Compare" 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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<tool file="filters/joiner.xml" />
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<tool file="filters/compare.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/ucsc_gene_bed_to_exon_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="Fetch Sequences and Alignments" id="extract">
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<tool file="extract/fasta-subseq-wrapper.xml" />
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<tool file="extract/extractAxt_wrapper.xml" />
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<tool file="extract/interval2maf.xml" />
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<tool file="extract/user_interval2maf.xml" />
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</section>
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<section name="Alignment Viewers" id="align_view">
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<tool file="visualization/GMAJ.xml" />
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<tool file="visualization/LAJ.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="operation">
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<tool file="operations/cluster.xml" />
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<tool file="operations/clusterMerge.xml" />
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<tool file="operations/interval_complement.xml" />
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<tool file="operations/complement.xml" />
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<tool file="operations/interval_coverage.xml" />
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<tool file="operations/covDensity.xml" />
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<tool file="operations/difference.xml" />
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<tool file="operations/intersect.xml" />
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<tool file="operations/joinLists.xml" />
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<tool file="operations/merge.xml" />
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<tool file="operations/overlap.xml" />
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<tool file="operations/proximity.xml" />
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<tool file="operations/subtract.xml" />
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<tool file="operations/unionWrapper.xml" />
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<tool file="operations/extend.xml" />
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</section>
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<section name="Operate on Genomic Intervals (bx)" 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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</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 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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</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" />
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<tool file="emboss/phylip/emboss_ekitsch.xml" />
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<tool file="emboss/phylip/emboss_emix.xml" />
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<tool file="emboss/phylip/emboss_eneighbor.xml" />
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<tool file="emboss/phylip/emboss_epenny.xml" />
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<tool file="emboss/phylip/emboss_eprotdist.xml" />
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<tool file="emboss/phylip/emboss_eprotpars.xml" />
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<tool file="emboss/phylip/emboss_erestml.xml" />
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<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="PAML" id="mdea">
|
|
<tool file="mdea/BaseML.xml" />
|
|
<tool file="mdea/AlphaSubst.xml" />
|
|
</section>
|
|
</toolbox>
|