mirror of
https://github.com/galaxyproject/galaxy.git
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Jeremy Goecks
bcc1e7b76c
gff_filter_by_feature_count tool filters a GFF file using conditions based on transcripts' features counts; for example, it is possible to filter for transcripts that have a minimum number of exons or transcripts that have 3' UTRs. Added GFF subheading to Tool Menu under Filtering and placed all GFF filtering tools under this heading.
445 lines
20 KiB
XML
445 lines
20 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/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="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 files" 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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</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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</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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</section>
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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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<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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</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="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="NGS: QC and manipulation" id="cshl_library_information">
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<label text="Illumina data" 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="Deprecated: Generic FASTQ data" id="fastq" />
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<tool file="next_gen_conversion/fastq_gen_conv.xml" />
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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="metag_tools/split_paired_reads.xml"
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<tool file="fastx_toolkit/fastq_to_fasta.xml" />
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-->
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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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</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/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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</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: Expression 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/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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</section>
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<section name="NGS: Peak Calling" id="peak_calling">
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<tool file="peak_calling/macs_wrapper.xml" />
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<tool file="genetrack/genetrack_indexer.xml" />
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<tool file="genetrack/genetrack_peak_prediction.xml" />
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</section>
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<section name="SNP/WGA: Data; Filters" id="rgdat">
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<label text="Data: Import and upload" id="rgimport" />
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<tool file="data_source/upload.xml"/>
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<tool file="data_source/access_libraries.xml" />
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<tool file="data_source/hapmapmart.xml" />
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<label text="Data: Filter and Clean" id="rgfilter" />
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<tool file="rgenetics/rgClean.xml"/>
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<tool file="rgenetics/rgPedSub.xml"/>
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<tool file="rgenetics/rgLDIndep.xml"/>
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<label text="Simulate" id="rgsim" />
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<tool file="rgenetics/rgfakePhe.xml"/>
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<tool file="rgenetics/rgfakePed.xml"/>
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</section>
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<section name="SNP/WGA: QC; LD; Plots" id="rgqcplot">
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<label text="QC; Eigenstrat" id="rgvisual" />
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<tool file="rgenetics/rgQC.xml"/>
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<tool file="rgenetics/rgEigPCA.xml"/>
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<label text="LD; Manhattan/QQ; GRR" id="rgld" />
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<tool file="rgenetics/rgHaploView.xml"/>
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<tool file="rgenetics/rgManQQ.xml"/>
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<tool file="rgenetics/rgGRR.xml"/>
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</section>
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<section name="SNP/WGA: Statistical Models" id="rgmodel">
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<tool file="rgenetics/rgCaCo.xml"/>
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<tool file="rgenetics/rgTDT.xml"/>
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<tool file="rgenetics/rgGLM.xml"/>
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<tool file="rgenetics/rgManQQ.xml"/>
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</section>
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<!--
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TODO: uncomment the following EMBOSS section whenever
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moving to test, but comment it in .sample to eliminate
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it from buildbot functional tests since these tools
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rarely change.
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-->
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<!--
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<section name="EMBOSS" id="EMBOSSLite">
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<tool file="emboss_5/emboss_antigenic.xml" />
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<tool file="emboss_5/emboss_backtranseq.xml" />
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<tool file="emboss_5/emboss_banana.xml" />
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<tool file="emboss_5/emboss_biosed.xml" />
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<tool file="emboss_5/emboss_btwisted.xml" />
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<tool file="emboss_5/emboss_cai_custom.xml" />
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<tool file="emboss_5/emboss_cai.xml" />
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<tool file="emboss_5/emboss_chaos.xml" />
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<tool file="emboss_5/emboss_charge.xml" />
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<tool file="emboss_5/emboss_checktrans.xml" />
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<tool file="emboss_5/emboss_chips.xml" />
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<tool file="emboss_5/emboss_cirdna.xml" />
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<tool file="emboss_5/emboss_codcmp.xml" />
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<tool file="emboss_5/emboss_coderet.xml" />
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<tool file="emboss_5/emboss_compseq.xml" />
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<tool file="emboss_5/emboss_cpgplot.xml" />
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<tool file="emboss_5/emboss_cpgreport.xml" />
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<tool file="emboss_5/emboss_cusp.xml" />
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<tool file="emboss_5/emboss_cutseq.xml" />
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<tool file="emboss_5/emboss_dan.xml" />
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<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>
|