mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
364180ef7d
TODO: A few new datatypes have been declared, but exist in name only (subclasses of Text defined only in datatypes_conf.xml), these should be refined to be true datatypes, with proper peeks, sniffing, metadata, etc. Help sections need work. HTML listing of files in e.g. Analyze Covariates should be prettified. Other items not listed.
551 lines
24 KiB
XML
551 lines
24 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/bx_browser.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/cbi_rice_mart.xml" />
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<tool file="data_source/gramene_mart.xml" />
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<tool file="data_source/fly_modencode.xml" />
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<tool file="data_source/flymine.xml" />
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<tool file="data_source/flymine_test.xml" />
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<tool file="data_source/modmine.xml" />
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<tool file="data_source/ratmine.xml" />
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<tool file="data_source/yeastmine.xml" />
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<tool file="data_source/metabolicmine.xml" />
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<tool file="data_source/worm_modencode.xml" />
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<tool file="data_source/wormbase.xml" />
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<tool file="data_source/wormbase_test.xml" />
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<tool file="data_source/eupathdb.xml" />
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<tool file="data_source/encode_db.xml" />
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<tool file="data_source/epigraph_import.xml" />
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<tool file="data_source/epigraph_import_test.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="Send Data" id="send">
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<tool file="data_destination/epigraph.xml" />
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<tool file="data_destination/epigraph_test.xml" />
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</section>
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<section name="ENCODE Tools" id="EncodeTools">
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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="Lift-Over" id="liftOver">
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<tool file="extract/liftOver_wrapper.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/cutWrapper.xml" />
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<tool file="filters/mergeCols.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/changeCase.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/randomlines.xml" />
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<tool file="filters/headWrapper.xml" />
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<tool file="filters/tailWrapper.xml" />
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<tool file="filters/trimmer.xml" />
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<tool file="filters/wc_gnu.xml" />
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<tool file="stats/dna_filtering.xml" />
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<tool file="new_operations/tables_arithmetic_operations.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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<label text="GFF" id="gff" />
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<tool file="filters/gff/extract_GFF_Features.xml" />
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<tool file="filters/gff/gff_filter_by_attribute.xml" />
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<tool file="filters/gff/gff_filter_by_feature_count.xml" />
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<tool file="filters/gff/gtf_filter_by_attribute_values_list.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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<tool file="new_operations/column_join.xml" />
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</section>
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<section name="Convert Formats" id="convert">
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<tool file="filters/axt_to_concat_fasta.xml" />
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<tool file="filters/axt_to_fasta.xml" />
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<tool file="filters/axt_to_lav.xml" />
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<tool file="filters/bed2gff.xml" />
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<tool file="fasta_tools/fasta_to_tabular.xml" />
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<tool file="filters/gff2bed.xml" />
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<tool file="filters/lav_to_bed.xml" />
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<tool file="maf/maf_to_bed.xml" />
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<tool file="maf/maf_to_interval.xml" />
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<tool file="maf/maf_to_fasta.xml" />
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<tool file="fasta_tools/tabular_to_fasta.xml" />
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<tool file="fastq/fastq_to_fasta.xml" />
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<tool file="filters/wiggle_to_simple.xml" />
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<tool file="filters/sff_extractor.xml" />
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<tool file="filters/gtf2bedgraph.xml" />
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<tool file="filters/wig_to_bigwig.xml" />
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<tool file="filters/bed_to_bigbed.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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</section>
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<section name="Fetch Sequences" id="fetchSeq">
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<tool file="extract/extract_genomic_dna.xml" />
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</section>
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<section name="Fetch Alignments" id="fetchAlign">
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<tool file="maf/interval2maf_pairwise.xml" />
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<tool file="maf/interval2maf.xml" />
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<tool file="maf/maf_split_by_species.xml"/>
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<tool file="maf/interval_maf_to_merged_fasta.xml" />
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<tool file="maf/genebed_maf_to_fasta.xml"/>
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<tool file="maf/maf_stats.xml"/>
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<tool file="maf/maf_thread_for_species.xml"/>
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<tool file="maf/maf_limit_to_species.xml"/>
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<tool file="maf/maf_limit_size.xml"/>
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<tool file="maf/maf_by_block_number.xml"/>
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<tool file="maf/maf_reverse_complement.xml"/>
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<tool file="maf/maf_filter.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" />
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<tool file="new_operations/subtract.xml" />
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<tool file="new_operations/merge.xml" />
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<tool file="new_operations/concat.xml" />
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<tool file="new_operations/basecoverage.xml" />
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<tool file="new_operations/coverage.xml" />
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<tool file="new_operations/complement.xml" />
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<tool file="new_operations/cluster.xml" id="cluster" />
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<tool file="new_operations/join.xml" />
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<tool file="new_operations/get_flanks.xml" />
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<tool file="new_operations/flanking_features.xml" />
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<tool file="annotation_profiler/annotation_profiler.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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<tool file="stats/generate_matrix_for_pca_lda.xml" />
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<tool file="stats/lda_analy.xml" />
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<tool file="stats/plot_from_lda.xml" />
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<tool file="regVariation/t_test_two_samples.xml" />
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<tool file="regVariation/compute_q_values.xml" />
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<label text="GFF" id="gff" />
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<tool file="stats/count_gff_features.xml" />
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</section>
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<!--
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Keep this section commented until all of the tools have functional tests
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<section name="Wavelet Analysis" id="dwt">
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<tool file="discreteWavelet/execute_dwt_IvC_all.xml" />
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<tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" />
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<tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" />
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<tool file="discreteWavelet/execute_dwt_var_perClass.xml" />
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</section>
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-->
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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/bar_chart.xml" />
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<tool file="plotting/xy_plot.xml" />
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<tool file="plotting/boxplot.xml" />
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<tool file="visualization/GMAJ.xml" />
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<tool file="visualization/LAJ.xml" />
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<tool file="visualization/build_ucsc_custom_track.xml" />
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<tool file="maf/vcf_to_maf_customtrack.xml" />
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<tool file="mutation/visualize.xml" />
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</section>
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<section name="Regional Variation" id="regVar">
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<tool file="regVariation/windowSplitter.xml" />
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<tool file="regVariation/featureCounter.xml" />
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<tool file="regVariation/quality_filter.xml" />
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<tool file="regVariation/maf_cpg_filter.xml" />
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<tool file="regVariation/getIndels_2way.xml" />
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<tool file="regVariation/getIndels_3way.xml" />
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<tool file="regVariation/getIndelRates_3way.xml" />
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<tool file="regVariation/substitutions.xml" />
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<tool file="regVariation/substitution_rates.xml" />
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<tool file="regVariation/microsats_alignment_level.xml" />
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<tool file="regVariation/microsats_mutability.xml" />
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<tool file="regVariation/delete_overlapping_indels.xml" />
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<tool file="regVariation/compute_motifs_frequency.xml" />
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<tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" />
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<tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s
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<tool file="regVariation/draw_stacked_barplots.xml" />
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<tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" />
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<tool file="regVariation/microsatellite_birthdeath.xml" />
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</section>
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<section name="Multiple regression" id="multReg">
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<tool file="regVariation/linear_regression.xml" />
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<tool file="regVariation/best_regression_subsets.xml" />
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<tool file="regVariation/rcve.xml" />
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</section>
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<section name="Multivariate Analysis" id="multVar">
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<tool file="multivariate_stats/pca.xml" />
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<tool file="multivariate_stats/cca.xml" />
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<tool file="multivariate_stats/kpca.xml" />
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<tool file="multivariate_stats/kcca.xml" />
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</section>
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<section name="Evolution" id="hyphy">
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<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
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<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
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<tool file="hyphy/hyphy_dnds_wrapper.xml" />
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<tool file="evolution/mutate_snp_codon.xml" />
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<tool file="evolution/codingSnps.xml" />
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<tool file="evolution/add_scores.xml" />
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</section>
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<section name="Motif Tools" id="motifs">
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<tool file="meme/meme.xml"/>
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<tool file="rgenetics/rgWebLogo3.xml" />
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</section>
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<section name="Multiple Alignments" id="clustal">
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<tool file="rgenetics/rgClustalw.xml" />
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</section>
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<section name="Metagenomic analyses" id="tax_manipulation">
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<tool file="taxonomy/gi2taxonomy.xml" />
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<tool file="taxonomy/t2t_report.xml" />
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<tool file="taxonomy/t2ps_wrapper.xml" />
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<tool file="taxonomy/find_diag_hits.xml" />
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<tool file="taxonomy/lca.xml" />
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<tool file="taxonomy/poisson2test.xml" />
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</section>
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<section name="FASTA manipulation" id="fasta_manipulation">
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<tool file="fasta_tools/fasta_compute_length.xml" />
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<tool file="fasta_tools/fasta_filter_by_length.xml" />
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<tool file="fasta_tools/fasta_concatenate_by_species.xml" />
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<tool file="fasta_tools/fasta_to_tabular.xml" />
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<tool file="fasta_tools/tabular_to_fasta.xml" />
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<tool file="fastx_toolkit/fasta_formatter.xml" />
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<tool file="fastx_toolkit/fasta_nucleotide_changer.xml" />
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<tool file="fastx_toolkit/fastx_collapser.xml" />
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</section>
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<section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
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<tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
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<tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
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<tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
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<tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
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<tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
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<tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
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</section>
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<section name="NGS: QC and manipulation" id="NGS_QC">
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<label text="FastQC: fastq/sam/bam" id="fastqcsambam" />
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<tool file="rgenetics/rgFastQC.xml" />
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<label text="QC/Metrics for sam/bam" id="qcsambam"/>
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<tool file="picard/picard_BamIndexStats.xml" />
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<tool file="picard/rgPicardASMetrics.xml" />
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<tool file="picard/rgPicardGCBiasMetrics.xml" />
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<tool file="picard/rgPicardLibComplexity.xml" />
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<tool file="picard/rgPicardInsertSize.xml" />
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<tool file="picard/rgPicardHsMetrics.xml" />
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<label text="bam/sam Cleaning" id="picard-tools" />
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<tool file="picard/picard_AddOrReplaceReadGroups.xml" />
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<tool file="picard/picard_ReorderSam.xml" />
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<tool file="picard/picard_ReplaceSamHeader.xml" />
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<tool file="picard/rgPicardFixMate.xml" />
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<tool file="picard/rgPicardMarkDups.xml" />
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<label text="Illumina fastq" id="illumina" />
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<tool file="fastq/fastq_groomer.xml" />
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<tool file="fastq/fastq_paired_end_splitter.xml" />
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<tool file="fastq/fastq_paired_end_joiner.xml" />
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<tool file="fastq/fastq_stats.xml" />
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<label text="Roche-454 data" id="454" />
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<tool file="metag_tools/short_reads_figure_score.xml" />
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<tool file="metag_tools/short_reads_trim_seq.xml" />
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<tool file="fastq/fastq_combiner.xml" />
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<label text="AB-SOLiD data" id="solid" />
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<tool file="next_gen_conversion/solid2fastq.xml" />
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<tool file="solid_tools/solid_qual_stats.xml" />
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<tool file="solid_tools/solid_qual_boxplot.xml" />
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<label text="Generic FASTQ manipulation" id="generic_fastq" />
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<tool file="fastq/fastq_filter.xml" />
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<tool file="fastq/fastq_trimmer.xml" />
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<tool file="fastq/fastq_trimmer_by_quality.xml" />
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<tool file="fastq/fastq_masker_by_quality.xml" />
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<tool file="fastq/fastq_manipulation.xml" />
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<tool file="fastq/fastq_to_fasta.xml" />
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<tool file="fastq/fastq_to_tabular.xml" />
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<tool file="fastq/tabular_to_fastq.xml" />
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<label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
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<tool file="fastx_toolkit/fastq_quality_converter.xml" />
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<tool file="fastx_toolkit/fastx_quality_statistics.xml" />
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<tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
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<tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
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<tool file="fastx_toolkit/fastq_to_fasta.xml" />
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<tool file="fastx_toolkit/fastq_quality_filter.xml" />
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<tool file="fastx_toolkit/fastq_to_fasta.xml" />
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<tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
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<tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
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<tool file="fastx_toolkit/fastx_clipper.xml" />
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<tool file="fastx_toolkit/fastx_collapser.xml" />
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<tool file="fastx_toolkit/fastx_renamer.xml" />
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<tool file="fastx_toolkit/fastx_reverse_complement.xml" />
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<tool file="fastx_toolkit/fastx_trimmer.xml" />
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</section>
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<!--
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Keep this section commented until it includes tools that
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will be hosted on test/main. The velvet wrappers have been
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included in the distribution but will not be hosted on our
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public servers for the current time.
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<section name="NGS: Assembly" id="ngs_assembly">
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<label text="Velvet" id="velvet"/>
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<tool file="sr_assembly/velvetg.xml" />
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<tool file="sr_assembly/velveth.xml" />
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</section>
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-->
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<section name="NGS: Mapping" id="solexa_tools">
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<tool file="sr_mapping/lastz_wrapper.xml" />
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<tool file="sr_mapping/lastz_paired_reads_wrapper.xml" />
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<tool file="sr_mapping/bowtie_wrapper.xml" />
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<tool file="sr_mapping/bowtie_color_wrapper.xml" />
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<tool file="sr_mapping/bwa_wrapper.xml" />
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<tool file="sr_mapping/bwa_color_wrapper.xml" />
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<tool file="sr_mapping/bfast_wrapper.xml" />
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<tool file="metag_tools/megablast_wrapper.xml" />
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<tool file="metag_tools/megablast_xml_parser.xml" />
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<tool file="sr_mapping/PerM.xml" />
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<tool file="sr_mapping/srma_wrapper.xml" />
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<tool file="sr_mapping/mosaik.xml"/>
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</section>
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<section name="NGS: Indel Analysis" id="indel_analysis">
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<tool file="indels/sam_indel_filter.xml" />
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<tool file="indels/indel_sam2interval.xml" />
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<tool file="indels/indel_table.xml" />
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<tool file="indels/indel_analysis.xml" />
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</section>
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<section name="NGS: RNA Analysis" id="ngs-rna-tools">
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<label text="RNA-seq" id="rna_seq" />
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<tool file="ngs_rna/tophat_wrapper.xml" />
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<tool file="ngs_rna/cufflinks_wrapper.xml" />
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<tool file="ngs_rna/cuffcompare_wrapper.xml" />
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<tool file="ngs_rna/cuffdiff_wrapper.xml" />
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<label text="Filtering" id="filtering" />
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<tool file="ngs_rna/filter_transcripts_via_tracking.xml" />
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</section>
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<section name="NGS: SAM Tools" id="samtools">
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<tool file="samtools/sam_bitwise_flag_filter.xml" />
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<tool file="samtools/sam2interval.xml" />
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<tool file="samtools/sam_to_bam.xml" />
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<tool file="samtools/bam_to_sam.xml" />
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<tool file="samtools/sam_merge.xml" />
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<tool file="samtools/sam_pileup.xml" />
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<tool file="samtools/pileup_parser.xml" />
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<tool file="samtools/pileup_interval.xml" />
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<tool file="samtools/samtools_flagstat.xml" />
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</section>
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<section name="NGS: GATK Tools" id="gatk">
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<label text="Realignment" id="gatk_realignment" />
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<tool file="gatk/realigner_target_creator.xml" />
|
|
<tool file="gatk/indel_realigner.xml" />
|
|
<label text="Base Recalibration" id="gatk_recalibration" />
|
|
<tool file="gatk/count_covariates.xml" />
|
|
<tool file="gatk/table_recalibration.xml" />
|
|
<tool file="gatk/analyze_covariates.xml" />
|
|
<label text="Genotyping" id="gatk_genotyping" />
|
|
<tool file="gatk/unified_genotyper.xml" />
|
|
</section>
|
|
<section name="NGS: Peak Calling" id="peak_calling">
|
|
<tool file="peak_calling/macs_wrapper.xml" />
|
|
<tool file="peak_calling/ccat_wrapper.xml" />
|
|
<tool file="genetrack/genetrack_indexer.xml" />
|
|
<tool file="genetrack/genetrack_peak_prediction.xml" />
|
|
</section>
|
|
<section name="NGS: Simulation" id="ngs-simulation">
|
|
<tool file="ngs_simulation/ngs_simulation.xml" />
|
|
</section>
|
|
<section name="SNP/WGA: Data; Filters" id="rgdat">
|
|
<label text="Data: Import and upload" id="rgimport" />
|
|
<tool file="data_source/upload.xml"/>
|
|
<tool file="data_source/access_libraries.xml" />
|
|
<label text="Data: Filter and Clean" id="rgfilter" />
|
|
<tool file="rgenetics/rgClean.xml"/>
|
|
<tool file="rgenetics/rgPedSub.xml"/>
|
|
<tool file="rgenetics/rgLDIndep.xml"/>
|
|
<label text="Simulate" id="rgsim" />
|
|
<tool file="rgenetics/rgfakePhe.xml"/>
|
|
<tool file="rgenetics/rgfakePed.xml"/>
|
|
</section>
|
|
<section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
|
|
<label text="QC; Eigenstrat" id="rgvisual" />
|
|
<tool file="rgenetics/rgQC.xml"/>
|
|
<tool file="rgenetics/rgEigPCA.xml"/>
|
|
<label text="LD; Manhattan/QQ; GRR" id="rgld" />
|
|
<tool file="rgenetics/rgHaploView.xml"/>
|
|
<tool file="rgenetics/rgManQQ.xml"/>
|
|
<tool file="rgenetics/rgGRR.xml"/>
|
|
</section>
|
|
<section name="SNP/WGA: Statistical Models" id="rgmodel">
|
|
<tool file="rgenetics/rgCaCo.xml"/>
|
|
<tool file="rgenetics/rgTDT.xml"/>
|
|
<tool file="rgenetics/rgGLM.xml"/>
|
|
<tool file="rgenetics/rgManQQ.xml"/>
|
|
</section>
|
|
<section name="Human Genome Variation" id="hgv">
|
|
<tool file="evolution/codingSnps.xml" />
|
|
<tool file="evolution/add_scores.xml" />
|
|
<tool file="human_genome_variation/sift.xml" />
|
|
<tool file="human_genome_variation/linkToGProfile.xml" />
|
|
<tool file="human_genome_variation/linkToDavid.xml"/>
|
|
<tool file="human_genome_variation/ctd.xml" />
|
|
<tool file="human_genome_variation/funDo.xml" />
|
|
<tool file="human_genome_variation/snpFreq.xml" />
|
|
<tool file="human_genome_variation/ldtools.xml" />
|
|
<tool file="human_genome_variation/pass.xml" />
|
|
<tool file="human_genome_variation/gpass.xml" />
|
|
<tool file="human_genome_variation/beam.xml" />
|
|
<tool file="human_genome_variation/lps.xml" />
|
|
<tool file="human_genome_variation/hilbertvis.xml" />
|
|
<tool file="human_genome_variation/freebayes.xml" />
|
|
</section>
|
|
<!--
|
|
This section can be uncommented on test, but the tools are not ready
|
|
for main.
|
|
-->
|
|
|
|
<!--
|
|
|
|
<section name="Genome Diversity" id="gd">
|
|
<tool file="genome_diversity/extract_primers.xml" />
|
|
<tool file="genome_diversity/select_snps.xml" />
|
|
<tool file="genome_diversity/select_restriction_enzymes.xml" />
|
|
<tool file="genome_diversity/extract_flanking_dna.xml" />
|
|
</section>
|
|
-->
|
|
|
|
<section name="VCF Tools" id="vcf_tools">
|
|
<tool file="vcf_tools/intersect.xml" />
|
|
<tool file="vcf_tools/annotate.xml" />
|
|
<tool file="vcf_tools/filter.xml" />
|
|
<tool file="vcf_tools/extract.xml" />
|
|
</section>
|
|
|
|
<!--
|
|
TODO: uncomment the following EMBOSS section whenever
|
|
moving to test, but comment it in .sample to eliminate
|
|
it from buildbot functional tests since these tools
|
|
rarely change.
|
|
-->
|
|
<!--
|
|
<section name="EMBOSS" id="EMBOSSLite">
|
|
<tool file="emboss_5/emboss_antigenic.xml" />
|
|
<tool file="emboss_5/emboss_backtranseq.xml" />
|
|
<tool file="emboss_5/emboss_banana.xml" />
|
|
<tool file="emboss_5/emboss_biosed.xml" />
|
|
<tool file="emboss_5/emboss_btwisted.xml" />
|
|
<tool file="emboss_5/emboss_cai_custom.xml" />
|
|
<tool file="emboss_5/emboss_cai.xml" />
|
|
<tool file="emboss_5/emboss_chaos.xml" />
|
|
<tool file="emboss_5/emboss_charge.xml" />
|
|
<tool file="emboss_5/emboss_checktrans.xml" />
|
|
<tool file="emboss_5/emboss_chips.xml" />
|
|
<tool file="emboss_5/emboss_cirdna.xml" />
|
|
<tool file="emboss_5/emboss_codcmp.xml" />
|
|
<tool file="emboss_5/emboss_coderet.xml" />
|
|
<tool file="emboss_5/emboss_compseq.xml" />
|
|
<tool file="emboss_5/emboss_cpgplot.xml" />
|
|
<tool file="emboss_5/emboss_cpgreport.xml" />
|
|
<tool file="emboss_5/emboss_cusp.xml" />
|
|
<tool file="emboss_5/emboss_cutseq.xml" />
|
|
<tool file="emboss_5/emboss_dan.xml" />
|
|
<tool file="emboss_5/emboss_degapseq.xml" />
|
|
<tool file="emboss_5/emboss_descseq.xml" />
|
|
<tool file="emboss_5/emboss_diffseq.xml" />
|
|
<tool file="emboss_5/emboss_digest.xml" />
|
|
<tool file="emboss_5/emboss_dotmatcher.xml" />
|
|
<tool file="emboss_5/emboss_dotpath.xml" />
|
|
<tool file="emboss_5/emboss_dottup.xml" />
|
|
<tool file="emboss_5/emboss_dreg.xml" />
|
|
<tool file="emboss_5/emboss_einverted.xml" />
|
|
<tool file="emboss_5/emboss_epestfind.xml" />
|
|
<tool file="emboss_5/emboss_equicktandem.xml" />
|
|
<tool file="emboss_5/emboss_est2genome.xml" />
|
|
<tool file="emboss_5/emboss_etandem.xml" />
|
|
<tool file="emboss_5/emboss_extractfeat.xml" />
|
|
<tool file="emboss_5/emboss_extractseq.xml" />
|
|
<tool file="emboss_5/emboss_freak.xml" />
|
|
<tool file="emboss_5/emboss_fuzznuc.xml" />
|
|
<tool file="emboss_5/emboss_fuzzpro.xml" />
|
|
<tool file="emboss_5/emboss_fuzztran.xml" />
|
|
<tool file="emboss_5/emboss_garnier.xml" />
|
|
<tool file="emboss_5/emboss_geecee.xml" />
|
|
<tool file="emboss_5/emboss_getorf.xml" />
|
|
<tool file="emboss_5/emboss_helixturnhelix.xml" />
|
|
<tool file="emboss_5/emboss_hmoment.xml" />
|
|
<tool file="emboss_5/emboss_iep.xml" />
|
|
<tool file="emboss_5/emboss_infoseq.xml" />
|
|
<tool file="emboss_5/emboss_isochore.xml" />
|
|
<tool file="emboss_5/emboss_lindna.xml" />
|
|
<tool file="emboss_5/emboss_marscan.xml" />
|
|
<tool file="emboss_5/emboss_maskfeat.xml" />
|
|
<tool file="emboss_5/emboss_maskseq.xml" />
|
|
<tool file="emboss_5/emboss_matcher.xml" />
|
|
<tool file="emboss_5/emboss_megamerger.xml" />
|
|
<tool file="emboss_5/emboss_merger.xml" />
|
|
<tool file="emboss_5/emboss_msbar.xml" />
|
|
<tool file="emboss_5/emboss_needle.xml" />
|
|
<tool file="emboss_5/emboss_newcpgreport.xml" />
|
|
<tool file="emboss_5/emboss_newcpgseek.xml" />
|
|
<tool file="emboss_5/emboss_newseq.xml" />
|
|
<tool file="emboss_5/emboss_noreturn.xml" />
|
|
<tool file="emboss_5/emboss_notseq.xml" />
|
|
<tool file="emboss_5/emboss_nthseq.xml" />
|
|
<tool file="emboss_5/emboss_octanol.xml" />
|
|
<tool file="emboss_5/emboss_oddcomp.xml" />
|
|
<tool file="emboss_5/emboss_palindrome.xml" />
|
|
<tool file="emboss_5/emboss_pasteseq.xml" />
|
|
<tool file="emboss_5/emboss_patmatdb.xml" />
|
|
<tool file="emboss_5/emboss_pepcoil.xml" />
|
|
<tool file="emboss_5/emboss_pepinfo.xml" />
|
|
<tool file="emboss_5/emboss_pepnet.xml" />
|
|
<tool file="emboss_5/emboss_pepstats.xml" />
|
|
<tool file="emboss_5/emboss_pepwheel.xml" />
|
|
<tool file="emboss_5/emboss_pepwindow.xml" />
|
|
<tool file="emboss_5/emboss_pepwindowall.xml" />
|
|
<tool file="emboss_5/emboss_plotcon.xml" />
|
|
<tool file="emboss_5/emboss_plotorf.xml" />
|
|
<tool file="emboss_5/emboss_polydot.xml" />
|
|
<tool file="emboss_5/emboss_preg.xml" />
|
|
<tool file="emboss_5/emboss_prettyplot.xml" />
|
|
<tool file="emboss_5/emboss_prettyseq.xml" />
|
|
<tool file="emboss_5/emboss_primersearch.xml" />
|
|
<tool file="emboss_5/emboss_revseq.xml" />
|
|
<tool file="emboss_5/emboss_seqmatchall.xml" />
|
|
<tool file="emboss_5/emboss_seqret.xml" />
|
|
<tool file="emboss_5/emboss_showfeat.xml" />
|
|
<tool file="emboss_5/emboss_shuffleseq.xml" />
|
|
<tool file="emboss_5/emboss_sigcleave.xml" />
|
|
<tool file="emboss_5/emboss_sirna.xml" />
|
|
<tool file="emboss_5/emboss_sixpack.xml" />
|
|
<tool file="emboss_5/emboss_skipseq.xml" />
|
|
<tool file="emboss_5/emboss_splitter.xml" />
|
|
<tool file="emboss_5/emboss_supermatcher.xml" />
|
|
<tool file="emboss_5/emboss_syco.xml" />
|
|
<tool file="emboss_5/emboss_tcode.xml" />
|
|
<tool file="emboss_5/emboss_textsearch.xml" />
|
|
<tool file="emboss_5/emboss_tmap.xml" />
|
|
<tool file="emboss_5/emboss_tranalign.xml" />
|
|
<tool file="emboss_5/emboss_transeq.xml" />
|
|
<tool file="emboss_5/emboss_trimest.xml" />
|
|
<tool file="emboss_5/emboss_trimseq.xml" />
|
|
<tool file="emboss_5/emboss_twofeat.xml" />
|
|
<tool file="emboss_5/emboss_union.xml" />
|
|
<tool file="emboss_5/emboss_vectorstrip.xml" />
|
|
<tool file="emboss_5/emboss_water.xml" />
|
|
<tool file="emboss_5/emboss_wobble.xml" />
|
|
<tool file="emboss_5/emboss_wordcount.xml" />
|
|
<tool file="emboss_5/emboss_wordmatch.xml" />
|
|
</section>
|
|
-->
|
|
</toolbox>
|