mirror of
https://github.com/galaxyproject/galaxy.git
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mvdbeek
126 lines
5.5 KiB
XML
126 lines
5.5 KiB
XML
<?xml version='1.0' encoding='utf-8'?>
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<toolbox monitor="true">
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<section id="getext" name="Get Data">
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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/ebi_sra.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/mousemine.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/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/zebrafishmine.xml" />
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<tool file="data_source/eupathdb.xml" />
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<tool file="data_source/hbvar.xml" />
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<tool file="genomespace/genomespace_importer.xml" />
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<tool file="genomespace/genomespace_push.xml" />
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</section>
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<section id="send" name="Send Data">
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<tool file="genomespace/genomespace_exporter.xml" />
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</section>
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<section id="collection_operations" name="Collection Operations">
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<tool file="${model_tools_path}/unzip_collection.xml" />
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<tool file="${model_tools_path}/zip_collection.xml" />
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<tool file="${model_tools_path}/filter_failed_collection.xml" />
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<tool file="${model_tools_path}/flatten_collection.xml" />
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<tool file="${model_tools_path}/merge_collection.xml" />
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<tool file="${model_tools_path}/relabel_from_file.xml" />
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<tool file="${model_tools_path}/filter_from_file.xml" />
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<tool file="${model_tools_path}/sort_collection_list.xml" />
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<tool file="${model_tools_path}/tag_collection_from_file.xml" />
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<tool file="${model_tools_path}/apply_rules.xml" />
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</section>
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<section id="liftOver" name="Lift-Over">
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<tool file="extract/liftOver_wrapper.xml" />
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</section>
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<section id="textutil" name="Text Manipulation">
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<tool file="filters/fixedValueColumn.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="filters/secure_hash_message_digest.xml" />
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</section>
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<section id="convert" name="Convert Formats">
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<tool file="filters/bed2gff.xml" />
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<tool file="filters/gff2bed.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="filters/sff_extractor.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 id="filter" name="Filter and Sort">
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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 id="gff" text="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 id="group" name="Join, Subtract and 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="stats/grouping.xml" />
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</section>
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<section id="fetchAlignSeq" name="Fetch Alignments/Sequences">
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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 id="bxops" name="Operate on Genomic Intervals" version="">
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<tool file="filters/wiggle_to_simple.xml" />
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<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
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<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
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</section>
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<section id="stats" name="Statistics">
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<tool file="stats/gsummary.xml" />
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<tool file="filters/uniq.xml" />
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</section>
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<section id="plots" name="Graph/Display Data">
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<tool file="maf/vcf_to_maf_customtrack.xml" />
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</section>
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<section id="hgv" name="Phenotype Association">
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<tool file="evolution/codingSnps.xml" />
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<tool file="evolution/add_scores.xml" />
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<tool file="phenotype_association/sift.xml" />
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<tool file="phenotype_association/linkToGProfile.xml" />
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<tool file="phenotype_association/linkToDavid.xml" />
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<tool file="phenotype_association/ldtools.xml" />
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<tool file="phenotype_association/pass.xml" />
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<tool file="phenotype_association/gpass.xml" />
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<tool file="phenotype_association/beam.xml" />
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<tool file="phenotype_association/lps.xml" />
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<tool file="phenotype_association/master2pg.xml" />
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</section>
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</toolbox>
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