| 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_archaea.xml" /> |
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| 7 | <tool file="data_source/bx_browser.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/gramene_mart.xml" /> |
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| 11 | <tool file="data_source/flymine.xml" /> |
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| 12 | <tool file="data_source/fly_modencode.xml" /> |
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| 13 | <tool file="data_source/ratmine.xml" /> |
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| 14 | <tool file="data_source/worm_modencode.xml" /> |
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| 15 | <tool file="data_source/wormbase.xml" /> |
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| 16 | <tool file="data_source/eupathdb.xml" /> |
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| 17 | <tool file="data_source/encode_db.xml" /> |
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| 18 | <tool file="data_source/epigraph_import.xml" /> |
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| 19 | </section> |
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| 20 | <section name="Send Data" id="send"> |
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| 21 | <tool file="data_destination/epigraph.xml" /> |
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| 22 | </section> |
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| 23 | <section name="ENCODE Tools" id="EncodeTools"> |
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| 24 | <tool file="encode/gencode_partition.xml" /> |
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| 25 | <tool file="encode/random_intervals.xml" /> |
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| 26 | </section> |
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| 27 | <section name="Lift-Over" id="liftOver"> |
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| 28 | <tool file="extract/liftOver_wrapper.xml" /> |
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| 29 | </section> |
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| 30 | <section name="Text Manipulation" id="textutil"> |
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| 31 | <tool file="filters/fixedValueColumn.xml" /> |
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| 32 | <tool file="stats/column_maker.xml" /> |
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| 33 | <tool file="filters/catWrapper.xml" /> |
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| 34 | <tool file="filters/condense_characters.xml" /> |
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| 35 | <tool file="filters/convert_characters.xml" /> |
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| 36 | <tool file="filters/mergeCols.xml" /> |
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| 37 | <tool file="filters/CreateInterval.xml" /> |
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| 38 | <tool file="filters/cutWrapper.xml" /> |
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| 39 | <tool file="filters/changeCase.xml" /> |
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| 40 | <tool file="filters/pasteWrapper.xml" /> |
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| 41 | <tool file="filters/remove_beginning.xml" /> |
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| 42 | <tool file="filters/randomlines.xml" /> |
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| 43 | <tool file="filters/headWrapper.xml" /> |
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| 44 | <tool file="filters/tailWrapper.xml" /> |
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| 45 | <tool file="filters/trimmer.xml" /> |
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| 46 | </section> |
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| 47 | <section name="Convert Formats" id="convert"> |
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| 48 | <tool file="filters/bed2gff.xml" /> |
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| 49 | <tool file="fasta_tools/fasta_to_tabular.xml" /> |
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| 50 | <tool file="filters/gff2bed.xml" /> |
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| 51 | <tool file="maf/maf_to_bed.xml" /> |
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| 52 | <tool file="maf/maf_to_interval.xml" /> |
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| 53 | <tool file="maf/maf_to_fasta.xml" /> |
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| 54 | <tool file="fasta_tools/tabular_to_fasta.xml" /> |
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| 55 | <tool file="fastq/fastq_to_fasta.xml" /> |
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| 56 | <tool file="filters/sff_extractor.xml" /> |
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| 57 | <tool file="filters/wig_to_bigwig.xml" /> |
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| 58 | </section> |
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| 59 | <section name="FASTA manipulation" id="fasta_manipulation"> |
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| 60 | <tool file="fasta_tools/fasta_compute_length.xml" /> |
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| 61 | <tool file="fasta_tools/fasta_filter_by_length.xml" /> |
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| 62 | <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> |
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| 63 | <tool file="fasta_tools/fasta_to_tabular.xml" /> |
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| 64 | <tool file="fasta_tools/tabular_to_fasta.xml" /> |
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| 65 | <tool file="fastx_toolkit/fasta_formatter.xml" /> |
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| 66 | <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> |
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| 67 | <tool file="fastx_toolkit/fastx_collapser.xml" /> |
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| 68 | </section> |
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| 69 | <section name="Filter and Sort" id="filter"> |
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| 70 | <tool file="stats/filtering.xml" /> |
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| 71 | <tool file="filters/sorter.xml" /> |
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| 72 | <tool file="filters/grep.xml" /> |
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| 73 | <tool file="stats/dna_filtering.xml" /> |
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| 74 | <label text="GFF" id="gff" /> |
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| 75 | <tool file="filters/gff/extract_GFF_Features.xml" /> |
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| 76 | <tool file="filters/gff/gff_filter_by_attribute.xml" /> |
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| 77 | <tool file="filters/gff/gff_filter_by_feature_count.xml" /> |
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| 78 | </section> |
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| 79 | <section name="Join, Subtract and Group" id="group"> |
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| 80 | <tool file="filters/joiner.xml" /> |
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| 81 | <tool file="filters/compare.xml"/> |
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| 82 | <tool file="new_operations/subtract_query.xml"/> |
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| 83 | <tool file="stats/grouping.xml" /> |
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| 84 | <tool file="new_operations/column_join.xml"/> |
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| 85 | </section> |
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| 86 | <section name="Extract Features" id="features"> |
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| 87 | <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> |
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| 88 | </section> |
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| 89 | <section name="Fetch Sequences" id="fetchSeq"> |
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| 90 | <tool file="extract/extract_genomic_dna.xml" /> |
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| 91 | </section> |
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| 92 | <section name="Fetch Alignments" id="fetchAlign"> |
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| 93 | <tool file="maf/interval2maf_pairwise.xml" /> |
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| 94 | <tool file="maf/interval2maf.xml" /> |
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| 95 | <tool file="maf/interval_maf_to_merged_fasta.xml" /> |
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| 96 | <tool file="maf/genebed_maf_to_fasta.xml"/> |
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| 97 | <tool file="maf/maf_stats.xml"/> |
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| 98 | <tool file="maf/maf_thread_for_species.xml"/> |
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| 99 | <tool file="maf/maf_limit_to_species.xml"/> |
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| 100 | <tool file="maf/maf_limit_size.xml"/> |
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| 101 | <tool file="maf/maf_by_block_number.xml"/> |
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| 102 | <tool file="maf/maf_filter.xml"/> |
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| 103 | <tool file="maf/maf_reverse_complement.xml"/> |
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| 104 | </section> |
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| 105 | <section name="Get Genomic Scores" id="scores"> |
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| 106 | <tool file="stats/wiggle_to_simple.xml" /> |
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| 107 | <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> |
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| 108 | <tool file="extract/phastOdds/phastOdds_tool.xml" /> |
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| 109 | </section> |
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| 110 | <section name="Operate on Genomic Intervals" id="bxops"> |
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| 111 | <tool file="new_operations/intersect.xml" /> |
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| 112 | <tool file="new_operations/subtract.xml" /> |
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| 113 | <tool file="new_operations/merge.xml" /> |
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| 114 | <tool file="new_operations/concat.xml" /> |
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| 115 | <tool file="new_operations/basecoverage.xml" /> |
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| 116 | <tool file="new_operations/coverage.xml" /> |
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| 117 | <tool file="new_operations/complement.xml" /> |
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| 118 | <tool file="new_operations/cluster.xml" id="cluster" /> |
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| 119 | <tool file="new_operations/join.xml" /> |
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| 120 | <tool file="new_operations/get_flanks.xml" /> |
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| 121 | <tool file="new_operations/flanking_features.xml" /> |
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| 122 | <tool file="annotation_profiler/annotation_profiler.xml" /> |
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| 123 | </section> |
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| 124 | <section name="Statistics" id="stats"> |
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| 125 | <tool file="stats/gsummary.xml" /> |
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| 126 | <tool file="filters/uniq.xml" /> |
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| 127 | <tool file="stats/cor.xml" /> |
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| 128 | </section> |
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| 129 | <section name="Graph/Display Data" id="plots"> |
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| 130 | <tool file="plotting/histogram2.xml" /> |
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| 131 | <tool file="plotting/scatterplot.xml" /> |
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| 132 | <tool file="plotting/xy_plot.xml" /> |
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| 133 | <tool file="plotting/boxplot.xml" /> |
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| 134 | <tool file="visualization/GMAJ.xml" /> |
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| 135 | <tool file="visualization/build_ucsc_custom_track.xml" /> |
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| 136 | <tool file="maf/vcf_to_maf_customtrack.xml" /> |
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| 137 | <tool file="mutation/visualize.xml" /> |
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| 138 | </section> |
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| 139 | <section name="Regional Variation" id="regVar"> |
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| 140 | <tool file="regVariation/windowSplitter.xml" /> |
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| 141 | <tool file="regVariation/featureCounter.xml" /> |
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| 142 | <tool file="regVariation/quality_filter.xml" /> |
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| 143 | <tool file="regVariation/maf_cpg_filter.xml" /> |
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| 144 | <tool file="regVariation/getIndels_2way.xml" /> |
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| 145 | <tool file="regVariation/getIndels_3way.xml" /> |
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| 146 | <tool file="regVariation/getIndelRates_3way.xml" /> |
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| 147 | <tool file="regVariation/substitutions.xml" /> |
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| 148 | <tool file="regVariation/substitution_rates.xml" /> |
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| 149 | <tool file="regVariation/microsats_alignment_level.xml" /> |
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| 150 | <tool file="regVariation/microsats_mutability.xml" /> |
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| 151 | </section> |
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| 152 | <section name="Multiple regression" id="multReg"> |
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| 153 | <tool file="regVariation/linear_regression.xml" /> |
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| 154 | <tool file="regVariation/best_regression_subsets.xml" /> |
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| 155 | <tool file="regVariation/rcve.xml" /> |
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| 156 | </section> |
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| 157 | <section name="Multivariate Analysis" id="multVar"> |
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| 158 | <tool file="multivariate_stats/pca.xml" /> |
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| 159 | <tool file="multivariate_stats/cca.xml" /> |
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| 160 | <tool file="multivariate_stats/kpca.xml" /> |
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| 161 | <tool file="multivariate_stats/kcca.xml" /> |
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| 162 | </section> |
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| 163 | <section name="Evolution" id="hyphy"> |
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| 164 | <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> |
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| 165 | <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> |
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| 166 | <!-- <tool file="hyphy/hyphy_dnds_wrapper.xml" /> --> |
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| 167 | <tool file="evolution/mutate_snp_codon.xml" /> |
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| 168 | </section> |
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| 169 | <section name="Metagenomic analyses" id="tax_manipulation"> |
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| 170 | <tool file="taxonomy/gi2taxonomy.xml" /> |
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| 171 | <tool file="taxonomy/t2t_report.xml" /> |
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| 172 | <tool file="taxonomy/t2ps_wrapper.xml" /> |
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| 173 | <tool file="taxonomy/find_diag_hits.xml" /> |
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| 174 | <tool file="taxonomy/lca.xml" /> |
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| 175 | <tool file="taxonomy/poisson2test.xml" /> |
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| 176 | </section> |
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| 177 | <section name="Human Genome Variation" id="hgv"> |
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| 178 | <tool file="evolution/codingSnps.xml" /> |
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| 179 | <tool file="evolution/add_scores.xml" /> |
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| 180 | <tool file="human_genome_variation/sift.xml" /> |
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| 181 | <tool file="human_genome_variation/linkToGProfile.xml" /> |
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| 182 | <tool file="human_genome_variation/linkToDavid.xml"/> |
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| 183 | <tool file="human_genome_variation/ctd.xml" /> |
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| 184 | <tool file="human_genome_variation/funDo.xml" /> |
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| 185 | <tool file="human_genome_variation/snpFreq.xml" /> |
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| 186 | <tool file="human_genome_variation/ldtools.xml" /> |
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| 187 | <tool file="human_genome_variation/pass.xml" /> |
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| 188 | <tool file="human_genome_variation/gpass.xml" /> |
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| 189 | <tool file="human_genome_variation/beam.xml" /> |
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| 190 | <tool file="human_genome_variation/lps.xml" /> |
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| 191 | <tool file="human_genome_variation/hilbertvis.xml" /> |
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| 192 | </section> |
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| 193 | <section name="EMBOSS" id="EMBOSSLite"> |
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| 194 | <tool file="emboss_5/emboss_antigenic.xml" /> |
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| 195 | <tool file="emboss_5/emboss_backtranseq.xml" /> |
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| 196 | <tool file="emboss_5/emboss_banana.xml" /> |
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| 197 | <tool file="emboss_5/emboss_biosed.xml" /> |
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| 198 | <tool file="emboss_5/emboss_btwisted.xml" /> |
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| 199 | <tool file="emboss_5/emboss_cai_custom.xml" /> |
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| 200 | <tool file="emboss_5/emboss_cai.xml" /> |
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| 201 | <tool file="emboss_5/emboss_chaos.xml" /> |
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| 202 | <tool file="emboss_5/emboss_charge.xml" /> |
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| 203 | <tool file="emboss_5/emboss_checktrans.xml" /> |
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| 204 | <tool file="emboss_5/emboss_chips.xml" /> |
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| 205 | <tool file="emboss_5/emboss_cirdna.xml" /> |
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| 206 | <tool file="emboss_5/emboss_codcmp.xml" /> |
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| 207 | <tool file="emboss_5/emboss_coderet.xml" /> |
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| 208 | <tool file="emboss_5/emboss_compseq.xml" /> |
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| 209 | <tool file="emboss_5/emboss_cpgplot.xml" /> |
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| 210 | <tool file="emboss_5/emboss_cpgreport.xml" /> |
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| 211 | <tool file="emboss_5/emboss_cusp.xml" /> |
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| 212 | <tool file="emboss_5/emboss_cutseq.xml" /> |
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| 213 | <tool file="emboss_5/emboss_dan.xml" /> |
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| 214 | <tool file="emboss_5/emboss_degapseq.xml" /> |
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| 215 | <tool file="emboss_5/emboss_descseq.xml" /> |
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| 216 | <tool file="emboss_5/emboss_diffseq.xml" /> |
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| 217 | <tool file="emboss_5/emboss_digest.xml" /> |
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| 218 | <tool file="emboss_5/emboss_dotmatcher.xml" /> |
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| 219 | <tool file="emboss_5/emboss_dotpath.xml" /> |
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| 220 | <tool file="emboss_5/emboss_dottup.xml" /> |
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| 221 | <tool file="emboss_5/emboss_dreg.xml" /> |
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| 222 | <tool file="emboss_5/emboss_einverted.xml" /> |
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| 223 | <tool file="emboss_5/emboss_epestfind.xml" /> |
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| 224 | <tool file="emboss_5/emboss_equicktandem.xml" /> |
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| 225 | <tool file="emboss_5/emboss_est2genome.xml" /> |
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| 226 | <tool file="emboss_5/emboss_etandem.xml" /> |
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| 227 | <tool file="emboss_5/emboss_extractfeat.xml" /> |
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| 228 | <tool file="emboss_5/emboss_extractseq.xml" /> |
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| 229 | <tool file="emboss_5/emboss_freak.xml" /> |
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| 230 | <tool file="emboss_5/emboss_fuzznuc.xml" /> |
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| 231 | <tool file="emboss_5/emboss_fuzzpro.xml" /> |
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| 232 | <tool file="emboss_5/emboss_fuzztran.xml" /> |
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| 233 | <tool file="emboss_5/emboss_garnier.xml" /> |
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| 234 | <tool file="emboss_5/emboss_geecee.xml" /> |
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| 235 | <tool file="emboss_5/emboss_getorf.xml" /> |
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| 236 | <tool file="emboss_5/emboss_helixturnhelix.xml" /> |
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| 237 | <tool file="emboss_5/emboss_hmoment.xml" /> |
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| 238 | <tool file="emboss_5/emboss_iep.xml" /> |
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| 239 | <tool file="emboss_5/emboss_infoseq.xml" /> |
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| 240 | <tool file="emboss_5/emboss_isochore.xml" /> |
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| 241 | <tool file="emboss_5/emboss_lindna.xml" /> |
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| 242 | <tool file="emboss_5/emboss_marscan.xml" /> |
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| 243 | <tool file="emboss_5/emboss_maskfeat.xml" /> |
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| 244 | <tool file="emboss_5/emboss_maskseq.xml" /> |
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| 245 | <tool file="emboss_5/emboss_matcher.xml" /> |
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| 246 | <tool file="emboss_5/emboss_megamerger.xml" /> |
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| 247 | <tool file="emboss_5/emboss_merger.xml" /> |
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| 248 | <tool file="emboss_5/emboss_msbar.xml" /> |
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| 249 | <tool file="emboss_5/emboss_needle.xml" /> |
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| 250 | <tool file="emboss_5/emboss_newcpgreport.xml" /> |
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| 251 | <tool file="emboss_5/emboss_newcpgseek.xml" /> |
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| 252 | <tool file="emboss_5/emboss_newseq.xml" /> |
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| 253 | <tool file="emboss_5/emboss_noreturn.xml" /> |
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| 254 | <tool file="emboss_5/emboss_notseq.xml" /> |
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| 255 | <tool file="emboss_5/emboss_nthseq.xml" /> |
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| 256 | <tool file="emboss_5/emboss_octanol.xml" /> |
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| 257 | <tool file="emboss_5/emboss_oddcomp.xml" /> |
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| 258 | <tool file="emboss_5/emboss_palindrome.xml" /> |
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| 259 | <tool file="emboss_5/emboss_pasteseq.xml" /> |
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| 260 | <tool file="emboss_5/emboss_patmatdb.xml" /> |
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| 261 | <tool file="emboss_5/emboss_pepcoil.xml" /> |
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| 262 | <tool file="emboss_5/emboss_pepinfo.xml" /> |
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| 263 | <tool file="emboss_5/emboss_pepnet.xml" /> |
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| 264 | <tool file="emboss_5/emboss_pepstats.xml" /> |
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| 265 | <tool file="emboss_5/emboss_pepwheel.xml" /> |
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| 266 | <tool file="emboss_5/emboss_pepwindow.xml" /> |
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| 267 | <tool file="emboss_5/emboss_pepwindowall.xml" /> |
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| 268 | <tool file="emboss_5/emboss_plotcon.xml" /> |
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| 269 | <tool file="emboss_5/emboss_plotorf.xml" /> |
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| 270 | <tool file="emboss_5/emboss_polydot.xml" /> |
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| 271 | <tool file="emboss_5/emboss_preg.xml" /> |
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| 272 | <tool file="emboss_5/emboss_prettyplot.xml" /> |
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| 273 | <tool file="emboss_5/emboss_prettyseq.xml" /> |
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| 274 | <tool file="emboss_5/emboss_primersearch.xml" /> |
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| 275 | <tool file="emboss_5/emboss_revseq.xml" /> |
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| 276 | <tool file="emboss_5/emboss_seqmatchall.xml" /> |
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| 277 | <tool file="emboss_5/emboss_seqret.xml" /> |
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| 278 | <tool file="emboss_5/emboss_showfeat.xml" /> |
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| 279 | <tool file="emboss_5/emboss_shuffleseq.xml" /> |
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| 280 | <tool file="emboss_5/emboss_sigcleave.xml" /> |
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| 281 | <tool file="emboss_5/emboss_sirna.xml" /> |
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| 282 | <tool file="emboss_5/emboss_sixpack.xml" /> |
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| 283 | <tool file="emboss_5/emboss_skipseq.xml" /> |
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| 284 | <tool file="emboss_5/emboss_splitter.xml" /> |
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| 285 | <tool file="emboss_5/emboss_supermatcher.xml" /> |
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| 286 | <tool file="emboss_5/emboss_syco.xml" /> |
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| 287 | <tool file="emboss_5/emboss_tcode.xml" /> |
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| 288 | <tool file="emboss_5/emboss_textsearch.xml" /> |
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| 289 | <tool file="emboss_5/emboss_tmap.xml" /> |
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| 290 | <tool file="emboss_5/emboss_tranalign.xml" /> |
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| 291 | <tool file="emboss_5/emboss_transeq.xml" /> |
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| 292 | <tool file="emboss_5/emboss_trimest.xml" /> |
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| 293 | <tool file="emboss_5/emboss_trimseq.xml" /> |
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| 294 | <tool file="emboss_5/emboss_twofeat.xml" /> |
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| 295 | <tool file="emboss_5/emboss_union.xml" /> |
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| 296 | <tool file="emboss_5/emboss_vectorstrip.xml" /> |
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| 297 | <tool file="emboss_5/emboss_water.xml" /> |
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| 298 | <tool file="emboss_5/emboss_wobble.xml" /> |
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| 299 | <tool file="emboss_5/emboss_wordcount.xml" /> |
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| 300 | <tool file="emboss_5/emboss_wordmatch.xml" /> |
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| 301 | </section> |
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| 302 | <label text="NGS Toolbox Beta" id="ngs" /> |
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| 303 | <section name="NGS: QC and manipulation" id="cshl_library_information"> |
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| 304 | <label text="Illumina data" id="illumina" /> |
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| 305 | <tool file="fastq/fastq_groomer.xml" /> |
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| 306 | <tool file="fastq/fastq_paired_end_splitter.xml" /> |
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| 307 | <tool file="fastq/fastq_paired_end_joiner.xml" /> |
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| 308 | <tool file="fastq/fastq_stats.xml" /> |
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| 309 | <label text="Roche-454 data" id="454" /> |
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| 310 | <tool file="metag_tools/short_reads_figure_score.xml" /> |
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| 311 | <tool file="metag_tools/short_reads_trim_seq.xml" /> |
|---|
| 312 | <tool file="fastq/fastq_combiner.xml" /> |
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| 313 | <label text="AB-SOLiD data" id="solid" /> |
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| 314 | <tool file="next_gen_conversion/solid2fastq.xml" /> |
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| 315 | <tool file="solid_tools/solid_qual_stats.xml" /> |
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| 316 | <tool file="solid_tools/solid_qual_boxplot.xml" /> |
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| 317 | <label text="Generic FASTQ manipulation" id="generic_fastq" /> |
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| 318 | <tool file="fastq/fastq_filter.xml" /> |
|---|
| 319 | <tool file="fastq/fastq_trimmer.xml" /> |
|---|
| 320 | <tool file="fastq/fastq_trimmer_by_quality.xml" /> |
|---|
| 321 | <tool file="fastq/fastq_masker_by_quality.xml" /> |
|---|
| 322 | <tool file="fastq/fastq_manipulation.xml" /> |
|---|
| 323 | <tool file="fastq/fastq_to_fasta.xml" /> |
|---|
| 324 | <tool file="fastq/fastq_to_tabular.xml" /> |
|---|
| 325 | <tool file="fastq/tabular_to_fastq.xml" /> |
|---|
| 326 | <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit_fastq" /> |
|---|
| 327 | <tool file="fastx_toolkit/fastq_quality_converter.xml" /> |
|---|
| 328 | <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> |
|---|
| 329 | <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> |
|---|
| 330 | <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> |
|---|
| 331 | <tool file="fastx_toolkit/fastq_to_fasta.xml" /> |
|---|
| 332 | <tool file="fastx_toolkit/fastq_quality_filter.xml" /> |
|---|
| 333 | <tool file="fastx_toolkit/fastq_to_fasta.xml" /> |
|---|
| 334 | <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> |
|---|
| 335 | <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> |
|---|
| 336 | <tool file="fastx_toolkit/fastx_clipper.xml" /> |
|---|
| 337 | <tool file="fastx_toolkit/fastx_collapser.xml" /> |
|---|
| 338 | <tool file="fastx_toolkit/fastx_renamer.xml" /> |
|---|
| 339 | <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> |
|---|
| 340 | <tool file="fastx_toolkit/fastx_trimmer.xml" /> |
|---|
| 341 | </section> |
|---|
| 342 | <section name="NGS: Mapping" id="ngs_mapping"> |
|---|
| 343 | <label text="Illumina" id="illumina"/> |
|---|
| 344 | <tool file="sr_mapping/bowtie_wrapper.xml" /> |
|---|
| 345 | <tool file="sr_mapping/bwa_wrapper.xml" /> |
|---|
| 346 | <label text="Roche-454" id="roche_454"/> |
|---|
| 347 | <tool file="sr_mapping/lastz_wrapper.xml" /> |
|---|
| 348 | <tool file="metag_tools/megablast_wrapper.xml" /> |
|---|
| 349 | <tool file="metag_tools/megablast_xml_parser.xml" /> |
|---|
| 350 | <label text="AB-SOLiD" id="ab_solid"/> |
|---|
| 351 | <tool file="sr_mapping/bowtie_color_wrapper.xml" /> |
|---|
| 352 | </section> |
|---|
| 353 | <section name="NGS: SAM Tools" id="samtools"> |
|---|
| 354 | <tool file="samtools/sam_bitwise_flag_filter.xml" /> |
|---|
| 355 | <tool file="samtools/sam2interval.xml" /> |
|---|
| 356 | <tool file="samtools/sam_to_bam.xml" /> |
|---|
| 357 | <tool file="samtools/bam_to_sam.xml" /> |
|---|
| 358 | <tool file="samtools/sam_merge.xml" /> |
|---|
| 359 | <tool file="samtools/sam_pileup.xml" /> |
|---|
| 360 | <tool file="samtools/pileup_parser.xml" /> |
|---|
| 361 | <tool file="samtools/pileup_interval.xml" /> |
|---|
| 362 | </section> |
|---|
| 363 | <section name="NGS: Indel Analysis" id="indel_analysis"> |
|---|
| 364 | <tool file="indels/sam_indel_filter.xml" /> |
|---|
| 365 | <tool file="indels/indel_sam2interval.xml" /> |
|---|
| 366 | <tool file="indels/indel_analysis.xml" /> |
|---|
| 367 | </section> |
|---|
| 368 | <section name="NGS: Peak Calling" id="peak_calling"> |
|---|
| 369 | <tool file="peak_calling/macs_wrapper.xml" /> |
|---|
| 370 | <tool file="genetrack/genetrack_indexer.xml" /> |
|---|
| 371 | <tool file="genetrack/genetrack_peak_prediction.xml" /> |
|---|
| 372 | </section> |
|---|
| 373 | <section name="NGS: RNA Analysis" id="ngs-rna-tools"> |
|---|
| 374 | <label text="RNA-seq" id="rna_seq" /> |
|---|
| 375 | <tool file="ngs_rna/tophat_wrapper.xml" /> |
|---|
| 376 | <tool file="ngs_rna/cufflinks_wrapper.xml" /> |
|---|
| 377 | <tool file="ngs_rna/cuffcompare_wrapper.xml" /> |
|---|
| 378 | <tool file="ngs_rna/cuffdiff_wrapper.xml" /> |
|---|
| 379 | <label text="Filtering" id="filtering" /> |
|---|
| 380 | <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> |
|---|
| 381 | </section> |
|---|
| 382 | <label text="RGENETICS" id="rgenetics" /> |
|---|
| 383 | <section name="SNP/WGA: Data; Filters" id="rgdat"> |
|---|
| 384 | <label text="Data: Import and upload" id="rgimport" /> |
|---|
| 385 | <tool file="data_source/upload.xml"/> |
|---|
| 386 | <tool file="data_source/access_libraries.xml" /> |
|---|
| 387 | <tool file="data_source/hapmapmart.xml" /> |
|---|
| 388 | <label text="Data: Filter and Clean" id="rgfilter" /> |
|---|
| 389 | <tool file="rgenetics/rgClean.xml"/> |
|---|
| 390 | <tool file="rgenetics/rgPedSub.xml"/> |
|---|
| 391 | <tool file="rgenetics/rgLDIndep.xml"/> |
|---|
| 392 | <label text="Simulate" id="rgsim" /> |
|---|
| 393 | <tool file="rgenetics/rgfakePhe.xml"/> |
|---|
| 394 | <tool file="rgenetics/rgfakePed.xml"/> |
|---|
| 395 | </section> |
|---|
| 396 | <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot"> |
|---|
| 397 | <label text="QC; Eigenstrat" id="rgvisual" /> |
|---|
| 398 | <tool file="rgenetics/rgQC.xml"/> |
|---|
| 399 | <tool file="rgenetics/rgEigPCA.xml"/> |
|---|
| 400 | <label text="LD; Manhattan/QQ; GRR" id="rgld" /> |
|---|
| 401 | <tool file="rgenetics/rgHaploView.xml"/> |
|---|
| 402 | <tool file="rgenetics/rgManQQ.xml"/> |
|---|
| 403 | <tool file="rgenetics/rgGRR.xml"/> |
|---|
| 404 | </section> |
|---|
| 405 | <section name="SNP/WGA: Statistical Models" id="rgmodel"> |
|---|
| 406 | <tool file="rgenetics/rgCaCo.xml"/> |
|---|
| 407 | <tool file="rgenetics/rgTDT.xml"/> |
|---|
| 408 | <tool file="rgenetics/rgGLM.xml"/> |
|---|
| 409 | <tool file="rgenetics/rgManQQ.xml"/> |
|---|
| 410 | </section> |
|---|
| 411 | </toolbox> |
|---|
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