| 1 |
<?xml version="1.0"?> |
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| 2 |
<toolbox> |
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| 3 |
<section name="Get Data" id="getext"> |
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| 4 |
<tool file="data_source/upload.xml"/> |
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| 5 |
<tool file="data_source/ucsc_tablebrowser.xml" /> |
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| 6 |
<tool file="data_source/ucsc_tablebrowser_test.xml" /> |
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| 7 |
<tool file="data_source/ucsc_tablebrowser_archaea.xml" /> |
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| 8 |
<tool file="data_source/microbial_import.xml" /> |
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| 9 |
<tool file="data_source/biomart.xml" /> |
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| 10 |
<tool file="data_source/biomart_test.xml" /> |
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| 11 |
<tool file="data_source/wormbase.xml" /> |
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| 12 |
<tool file="data_source/wormbase_test.xml" /> |
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| 13 |
<tool file="data_source/flymine.xml" /> |
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| 14 |
<tool file="data_source/encode_db.xml" /> |
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| 15 |
<tool file="data_source/epigraph_import.xml" /> |
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| 16 |
<tool file="data_source/epigraph_import_test.xml" /> |
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| 17 |
<tool file="data_source/hbvar.xml" /> |
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| 18 |
<tool file="validation/fix_errors.xml" /> |
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| 19 |
</section> |
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| 20 |
<section name="Get ENCODE Data" id="encode"> |
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| 21 |
<tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/> |
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| 22 |
<tool file="data_source/encode_import_genes_and_transcripts.xml"/> |
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| 23 |
<tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/> |
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| 24 |
<tool file="data_source/encode_import_transcription_regulation.xml"/> |
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| 25 |
<tool file="data_source/encode_import_all_latest_datasets.xml" /> |
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| 26 |
<tool file="data_source/encode_import_gencode.xml" /> |
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| 27 |
</section> |
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| 28 |
<section name="Send Data" id="send"> |
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| 29 |
<tool file="data_destination/epigraph.xml" /> |
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| 30 |
<tool file="data_destination/epigraph_test.xml" /> |
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| 31 |
</section> |
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| 32 |
<section name="ENCODE Tools" id="EncodeTools"> |
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| 33 |
<tool file="encode/gencode_partition.xml" /> |
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| 34 |
<tool file="encode/random_intervals.xml" /> |
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| 35 |
</section> |
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| 36 |
<section name="Lift-Over" id="liftOver"> |
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| 37 |
<tool file="extract/liftOver_wrapper.xml" /> |
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| 38 |
</section> |
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| 39 |
<section name="Text Manipulation" id="textutil"> |
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| 40 |
<tool file="filters/fixedValueColumn.xml" /> |
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| 41 |
<tool file="stats/column_maker.xml" /> |
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| 42 |
<tool file="filters/catWrapper.xml" /> |
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| 43 |
<tool file="filters/condense_characters.xml" /> |
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| 44 |
<tool file="filters/convert_characters.xml" /> |
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| 45 |
<tool file="filters/CreateInterval.xml" /> |
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| 46 |
<tool file="filters/cutWrapper.xml" /> |
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| 47 |
<tool file="filters/changeCase.xml" /> |
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| 48 |
<tool file="filters/pasteWrapper.xml" /> |
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| 49 |
<tool file="filters/remove_beginning.xml" /> |
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| 50 |
<tool file="filters/headWrapper.xml" /> |
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| 51 |
<tool file="filters/tailWrapper.xml" /> |
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| 52 |
</section> |
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| 53 |
<section name="Filter and Sort" id="filter"> |
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| 54 |
<tool file="stats/filtering.xml" /> |
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| 55 |
<tool file="filters/sorter.xml" /> |
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| 56 |
<tool file="filters/grep.xml" /> |
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| 57 |
</section> |
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| 58 |
<section name="Join, Subtract and Group" id="group"> |
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| 59 |
<tool file="filters/joiner.xml" /> |
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| 60 |
<tool file="filters/compare.xml"/> |
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| 61 |
<tool file="new_operations/subtract_query.xml"/> |
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| 62 |
<tool file="stats/grouping.xml" /> |
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| 63 |
</section> |
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| 64 |
<section name="Convert Formats" id="convert"> |
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| 65 |
<tool file="filters/axt_to_concat_fasta.xml" /> |
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| 66 |
<tool file="filters/axt_to_fasta.xml" /> |
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| 67 |
<tool file="filters/axt_to_lav.xml" /> |
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| 68 |
<tool file="filters/bed2gff.xml" /> |
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| 69 |
<tool file="fasta_tools/fasta_to_tabular.xml" /> |
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| 70 |
<tool file="metag_tools/fastqsolexa_to_fasta_qual.xml" /> |
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| 71 |
<tool file="filters/gff2bed.xml" /> |
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| 72 |
<tool file="filters/lav_to_bed.xml" /> |
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| 73 |
<tool file="maf/maf_to_bed.xml" /> |
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| 74 |
<tool file="maf/maf_to_fasta.xml" /> |
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| 75 |
<tool file="fasta_tools/tabular_to_fasta.xml" /> |
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| 76 |
</section> |
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| 77 |
<section name="Extract Features" id="features"> |
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| 78 |
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> |
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| 79 |
<tool file="extract/extract_GFF_Features.xml" /> |
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| 80 |
</section> |
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| 81 |
<section name="Fetch Sequences" id="fetchSeq"> |
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| 82 |
<tool file="extract/extract_genomic_dna.xml" /> |
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| 83 |
</section> |
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| 84 |
<section name="Fetch Alignments" id="fetchAlign"> |
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| 85 |
<tool file="maf/interval2maf_pairwise.xml" /> |
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| 86 |
<tool file="maf/interval2maf.xml" /> |
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| 87 |
<tool file="maf/interval_maf_to_merged_fasta.xml" /> |
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| 88 |
<tool file="maf/genebed_maf_to_fasta.xml"/> |
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| 89 |
<tool file="maf/maf_stats.xml"/> |
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| 90 |
<tool file="maf/maf_thread_for_species.xml"/> |
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| 91 |
<tool file="maf/maf_limit_to_species.xml"/> |
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| 92 |
<tool file="maf/maf_limit_size.xml"/> |
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| 93 |
<tool file="maf/maf_by_block_number.xml"/> |
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| 94 |
<tool file="maf/maf_reverse_complement.xml"/> |
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| 95 |
<tool file="maf/maf_filter.xml"/> |
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| 96 |
</section> |
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| 97 |
<section name="Get Genomic Scores" id="scores"> |
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| 98 |
<tool file="stats/wiggle_to_simple.xml" /> |
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| 99 |
<tool file="stats/aggregate_binned_scores_in_intervals.xml" /> |
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| 100 |
<tool file="extract/phastOdds/phastOdds_tool.xml" /> |
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| 101 |
</section> |
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| 102 |
<section name="Operate on Genomic Intervals" id="bxops"> |
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| 103 |
<tool file="new_operations/intersect.xml" /> |
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| 104 |
<tool file="new_operations/subtract.xml" /> |
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| 105 |
<tool file="new_operations/merge.xml" /> |
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| 106 |
<tool file="new_operations/concat.xml" /> |
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| 107 |
<tool file="new_operations/basecoverage.xml" /> |
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| 108 |
<tool file="new_operations/coverage.xml" /> |
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| 109 |
<tool file="new_operations/complement.xml" /> |
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| 110 |
<tool file="new_operations/cluster.xml" id="cluster" /> |
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| 111 |
<tool file="new_operations/join.xml" /> |
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| 112 |
<tool file="new_operations/get_flanks.xml" /> |
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| 113 |
<tool file="new_operations/flanking_features.xml" /> |
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| 114 |
<tool file="annotation_profiler/annotation_profiler.xml" /> |
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| 115 |
</section> |
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| 116 |
<section name="Statistics" id="stats"> |
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| 117 |
<tool file="stats/gsummary.xml" /> |
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| 118 |
<tool file="filters/uniq.xml" /> |
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| 119 |
<tool file="stats/cor.xml" /> |
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| 120 |
</section> |
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| 121 |
<section name="Graph/Display Data" id="plots"> |
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| 122 |
<tool file="plotting/histogram2.xml" /> |
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| 123 |
<tool file="plotting/scatterplot.xml" /> |
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| 124 |
<tool file="plotting/bar_chart.xml" /> |
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| 125 |
<tool file="plotting/xy_plot.xml" /> |
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| 126 |
<tool file="visualization/GMAJ.xml" /> |
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| 127 |
<tool file="visualization/LAJ.xml" /> |
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| 128 |
<tool file="visualization/build_ucsc_custom_track.xml" /> |
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| 129 |
</section> |
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| 130 |
<section name="Regional Variation" id="regVar"> |
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| 131 |
<tool file="regVariation/windowSplitter.xml" /> |
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| 132 |
<tool file="regVariation/featureCounter.xml" /> |
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| 133 |
<tool file="regVariation/quality_filter.xml" /> |
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| 134 |
<tool file="regVariation/maf_cpg_filter.xml" /> |
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| 135 |
<tool file="regVariation/getIndels_2way.xml" /> |
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| 136 |
<tool file="regVariation/getIndels_3way.xml" /> |
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| 137 |
<tool file="regVariation/getIndelRates_3way.xml" /> |
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| 138 |
<tool file="regVariation/substitutions.xml" /> |
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| 139 |
<tool file="regVariation/substitution_rates.xml" /> |
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| 140 |
<tool file="regVariation/microsats_alignment_level.xml" /> |
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| 141 |
<tool file="regVariation/microsats_mutability.xml" /> |
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| 142 |
</section> |
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| 143 |
<section name="Multiple regression" id="multReg"> |
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| 144 |
<tool file="regVariation/linear_regression.xml" /> |
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| 145 |
<tool file="regVariation/best_regression_subsets.xml" /> |
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| 146 |
<tool file="regVariation/rcve.xml" /> |
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| 147 |
</section> |
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| 148 |
<section name="Evolution: HyPhy" id="hyphy"> |
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| 149 |
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> |
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| 150 |
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> |
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| 151 |
<tool file="hyphy/hyphy_dnds_wrapper.xml" /> |
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| 152 |
</section> |
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| 153 |
<section name="Taxonomy manipulation" id="tax_manipulation"> |
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| 154 |
<tool file="taxonomy/gi2taxonomy.xml" /> |
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| 155 |
<tool file="taxonomy/t2t_report.xml" /> |
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| 156 |
<tool file="taxonomy/t2ps_wrapper.xml" /> |
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| 157 |
<tool file="taxonomy/find_diag_hits.xml" /> |
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| 158 |
<tool file="taxonomy/poisson2test.xml" /> |
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| 159 |
</section> |
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| 160 |
<section name="Solexa tools" id="solexa_tools"> |
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| 161 |
<tool file="sr_mapping/fastq_statistics.xml" /> |
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| 162 |
<tool file="sr_mapping/lastz_wrapper.xml" /> |
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| 163 |
</section> |
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| 164 |
<!-- |
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| 165 |
TODO: uncomment the following EMBOSS section whenever |
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| 166 |
moving to test, but comment it in .sample to eliminate |
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| 167 |
it from buildbot functional tests since these tools |
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| 168 |
rarely change. |
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| 169 |
--> |
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| 170 |
<!-- |
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| 171 |
<section name="EMBOSS" id="EMBOSSLite"> |
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| 172 |
<tool file="emboss_5/emboss_antigenic.xml" /> |
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| 173 |
<tool file="emboss_5/emboss_backtranseq.xml" /> |
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| 174 |
<tool file="emboss_5/emboss_banana.xml" /> |
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| 175 |
<tool file="emboss_5/emboss_biosed.xml" /> |
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| 176 |
<tool file="emboss_5/emboss_btwisted.xml" /> |
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| 177 |
<tool file="emboss_5/emboss_cai_custom.xml" /> |
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| 178 |
<tool file="emboss_5/emboss_cai.xml" /> |
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| 179 |
<tool file="emboss_5/emboss_chaos.xml" /> |
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| 180 |
<tool file="emboss_5/emboss_charge.xml" /> |
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| 181 |
<tool file="emboss_5/emboss_checktrans.xml" /> |
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| 182 |
<tool file="emboss_5/emboss_chips.xml" /> |
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| 183 |
<tool file="emboss_5/emboss_cirdna.xml" /> |
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| 184 |
<tool file="emboss_5/emboss_codcmp.xml" /> |
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| 185 |
<tool file="emboss_5/emboss_coderet.xml" /> |
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| 186 |
<tool file="emboss_5/emboss_compseq.xml" /> |
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| 187 |
<tool file="emboss_5/emboss_cpgplot.xml" /> |
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| 188 |
<tool file="emboss_5/emboss_cpgreport.xml" /> |
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| 189 |
<tool file="emboss_5/emboss_cusp.xml" /> |
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| 190 |
<tool file="emboss_5/emboss_cutseq.xml" /> |
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| 191 |
<tool file="emboss_5/emboss_dan.xml" /> |
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| 192 |
<tool file="emboss_5/emboss_degapseq.xml" /> |
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| 193 |
<tool file="emboss_5/emboss_descseq.xml" /> |
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| 194 |
<tool file="emboss_5/emboss_diffseq.xml" /> |
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| 195 |
<tool file="emboss_5/emboss_digest.xml" /> |
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| 196 |
<tool file="emboss_5/emboss_dotmatcher.xml" /> |
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| 197 |
<tool file="emboss_5/emboss_dotpath.xml" /> |
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| 198 |
<tool file="emboss_5/emboss_dottup.xml" /> |
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| 199 |
<tool file="emboss_5/emboss_dreg.xml" /> |
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| 200 |
<tool file="emboss_5/emboss_einverted.xml" /> |
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| 201 |
<tool file="emboss_5/emboss_epestfind.xml" /> |
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| 202 |
<tool file="emboss_5/emboss_equicktandem.xml" /> |
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| 203 |
<tool file="emboss_5/emboss_est2genome.xml" /> |
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| 204 |
<tool file="emboss_5/emboss_etandem.xml" /> |
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| 205 |
<tool file="emboss_5/emboss_extractfeat.xml" /> |
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| 206 |
<tool file="emboss_5/emboss_extractseq.xml" /> |
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| 207 |
<tool file="emboss_5/emboss_freak.xml" /> |
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| 208 |
<tool file="emboss_5/emboss_fuzznuc.xml" /> |
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| 209 |
<tool file="emboss_5/emboss_fuzzpro.xml" /> |
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| 210 |
<tool file="emboss_5/emboss_fuzztran.xml" /> |
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| 211 |
<tool file="emboss_5/emboss_garnier.xml" /> |
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| 212 |
<tool file="emboss_5/emboss_geecee.xml" /> |
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| 213 |
<tool file="emboss_5/emboss_getorf.xml" /> |
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| 214 |
<tool file="emboss_5/emboss_helixturnhelix.xml" /> |
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| 215 |
<tool file="emboss_5/emboss_hmoment.xml" /> |
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| 216 |
<tool file="emboss_5/emboss_iep.xml" /> |
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| 217 |
<tool file="emboss_5/emboss_infoseq.xml" /> |
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| 218 |
<tool file="emboss_5/emboss_isochore.xml" /> |
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| 219 |
<tool file="emboss_5/emboss_lindna.xml" /> |
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| 220 |
<tool file="emboss_5/emboss_marscan.xml" /> |
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| 221 |
<tool file="emboss_5/emboss_maskfeat.xml" /> |
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| 222 |
<tool file="emboss_5/emboss_maskseq.xml" /> |
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| 223 |
<tool file="emboss_5/emboss_matcher.xml" /> |
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| 224 |
<tool file="emboss_5/emboss_megamerger.xml" /> |
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| 225 |
<tool file="emboss_5/emboss_merger.xml" /> |
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| 226 |
<tool file="emboss_5/emboss_msbar.xml" /> |
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| 227 |
<tool file="emboss_5/emboss_needle.xml" /> |
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| 228 |
<tool file="emboss_5/emboss_newcpgreport.xml" /> |
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| 229 |
<tool file="emboss_5/emboss_newcpgseek.xml" /> |
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| 230 |
<tool file="emboss_5/emboss_newseq.xml" /> |
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| 231 |
<tool file="emboss_5/emboss_noreturn.xml" /> |
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| 232 |
<tool file="emboss_5/emboss_notseq.xml" /> |
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| 233 |
<tool file="emboss_5/emboss_nthseq.xml" /> |
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| 234 |
<tool file="emboss_5/emboss_octanol.xml" /> |
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| 235 |
<tool file="emboss_5/emboss_oddcomp.xml" /> |
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| 236 |
<tool file="emboss_5/emboss_palindrome.xml" /> |
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| 237 |
<tool file="emboss_5/emboss_pasteseq.xml" /> |
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| 238 |
<tool file="emboss_5/emboss_patmatdb.xml" /> |
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| 239 |
<tool file="emboss_5/emboss_pepcoil.xml" /> |
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| 240 |
<tool file="emboss_5/emboss_pepinfo.xml" /> |
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| 241 |
<tool file="emboss_5/emboss_pepnet.xml" /> |
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| 242 |
<tool file="emboss_5/emboss_pepstats.xml" /> |
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| 243 |
<tool file="emboss_5/emboss_pepwheel.xml" /> |
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| 244 |
<tool file="emboss_5/emboss_pepwindow.xml" /> |
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| 245 |
<tool file="emboss_5/emboss_pepwindowall.xml" /> |
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| 246 |
<tool file="emboss_5/emboss_plotcon.xml" /> |
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| 247 |
<tool file="emboss_5/emboss_plotorf.xml" /> |
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| 248 |
<tool file="emboss_5/emboss_polydot.xml" /> |
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| 249 |
<tool file="emboss_5/emboss_preg.xml" /> |
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| 250 |
<tool file="emboss_5/emboss_prettyplot.xml" /> |
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| 251 |
<tool file="emboss_5/emboss_prettyseq.xml" /> |
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| 252 |
<tool file="emboss_5/emboss_primersearch.xml" /> |
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| 253 |
<tool file="emboss_5/emboss_revseq.xml" /> |
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| 254 |
<tool file="emboss_5/emboss_seqmatchall.xml" /> |
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| 255 |
<tool file="emboss_5/emboss_seqret.xml" /> |
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| 256 |
<tool file="emboss_5/emboss_showfeat.xml" /> |
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| 257 |
<tool file="emboss_5/emboss_shuffleseq.xml" /> |
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| 258 |
<tool file="emboss_5/emboss_sigcleave.xml" /> |
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| 259 |
<tool file="emboss_5/emboss_sirna.xml" /> |
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| 260 |
<tool file="emboss_5/emboss_sixpack.xml" /> |
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| 261 |
<tool file="emboss_5/emboss_skipseq.xml" /> |
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| 262 |
<tool file="emboss_5/emboss_splitter.xml" /> |
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| 263 |
<tool file="emboss_5/emboss_supermatcher.xml" /> |
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| 264 |
<tool file="emboss_5/emboss_syco.xml" /> |
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| 265 |
<tool file="emboss_5/emboss_tcode.xml" /> |
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| 266 |
<tool file="emboss_5/emboss_textsearch.xml" /> |
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| 267 |
<tool file="emboss_5/emboss_tmap.xml" /> |
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| 268 |
<tool file="emboss_5/emboss_tranalign.xml" /> |
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| 269 |
<tool file="emboss_5/emboss_transeq.xml" /> |
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| 270 |
<tool file="emboss_5/emboss_trimest.xml" /> |
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| 271 |
<tool file="emboss_5/emboss_trimseq.xml" /> |
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| 272 |
<tool file="emboss_5/emboss_twofeat.xml" /> |
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| 273 |
<tool file="emboss_5/emboss_union.xml" /> |
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| 274 |
<tool file="emboss_5/emboss_vectorstrip.xml" /> |
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| 275 |
<tool file="emboss_5/emboss_water.xml" /> |
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| 276 |
<tool file="emboss_5/emboss_wobble.xml" /> |
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| 277 |
<tool file="emboss_5/emboss_wordcount.xml" /> |
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| 278 |
<tool file="emboss_5/emboss_wordmatch.xml" /> |
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| 279 |
</section> |
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| 280 |
--> |
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| 281 |
<section name="FASTA manipulation" id="fasta_manipulation"> |
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| 282 |
<tool file="fasta_tools/fasta_compute_length.xml" /> |
|---|
| 283 |
<tool file="fasta_tools/fasta_filter_by_length.xml" /> |
|---|
| 284 |
<tool file="fasta_tools/fasta_concatenate_by_species.xml" /> |
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| 285 |
<tool file="fasta_tools/fasta_to_tabular.xml" /> |
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| 286 |
<tool file="fasta_tools/tabular_to_fasta.xml" /> |
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| 287 |
</section> |
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| 288 |
<section name="Short Read QC and Manipulation" id="short_read_analysis"> |
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| 289 |
<tool file="metag_tools/short_reads_figure_score.xml" /> |
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| 290 |
<tool file="metag_tools/short_reads_figure_high_quality_length.xml" /> |
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| 291 |
<tool file="metag_tools/short_reads_trim_seq.xml" /> |
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| 292 |
<tool file="metag_tools/blat_coverage_report.xml" /> |
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| 293 |
<tool file="metag_tools/split_paired_reads.xml" /> |
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| 294 |
</section> |
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| 295 |
<section name="Short Read Mapping" id="solexa_tools"> |
|---|
| 296 |
<tool file="metag_tools/shrimp_color_wrapper.xml" /> |
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| 297 |
<tool file="metag_tools/shrimp_wrapper.xml" /> |
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| 298 |
<tool file="sr_mapping/lastz_wrapper.xml" /> |
|---|
| 299 |
<tool file="metag_tools/megablast_wrapper.xml" /> |
|---|
| 300 |
<tool file="metag_tools/megablast_xml_parser.xml" /> |
|---|
| 301 |
<tool file="metag_tools/blat_wrapper.xml" /> |
|---|
| 302 |
<tool file="metag_tools/mapping_to_ucsc.xml" /> |
|---|
| 303 |
</section> |
|---|
| 304 |
</toolbox> |
|---|
Galaxy