integrated_tool_panel.xml

<?xml version="1.0"?>
<toolbox>
    <!--
    This is Galaxy's integrated tool panel and should be modified directly only for
    reordering tools inside a section. Each time Galaxy starts up, this file is
    synchronized with the various tool config files: tools, sections and labels
    added to one of these files, will be added also here in the appropriate place,
    while elements removed from the tool config files will be correspondingly
    deleted from this file.
    To modify locally managed tools (e.g. from tool_conf.xml) modify that file
    directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g.
    from shed_tool_conf.xml) should be managed from within the Galaxy interface or
    via its API - but if changes are necessary (such as to hide a tool or re-assign
    its section) modify that file and restart Galaxy.
    -->
    <section id="get_data" name="Get Data" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.9+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.9+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.9+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.8+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.8+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.7+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.7+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.7+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.7+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.7+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.7+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.5+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gdcwebapp/data_source_gdcwebapp/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.10.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.10.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.10.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.4" />

        <tool id="sra_source" />

        <tool id="modENCODEfly" />

        <tool id="intermine" />

        <tool id="upload1" />

        <tool id="ucsc_table_direct1" />

        <tool id="mousemine" />

        <tool id="ucsc_table_direct_archaea1" />

        <tool id="yeastmine" />

        <tool id="modENCODEworm" />

        <tool id="wormbase" />

        <tool id="ebi_sra_main" />

        <tool id="flymine" />

        <tool id="ratmine" />

        <tool id="zebrafishmine" />

        <tool id="hbvar" />

        <tool id="modmine" />

    </section>

    <section id="send_data" name="Send Data" version="">

    </section>

    <section id="collection_operations" name="Collection Operations" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.1" />

        <tool id="__UNZIP_COLLECTION__" />

        <tool id="__ZIP_COLLECTION__" />

        <tool id="__FILTER_FAILED_DATASETS__" />

        <tool id="__FLATTEN__" />

        <tool id="__FILTER_EMPTY_DATASETS__" />

        <tool id="__MERGE_COLLECTION__" />

        <tool id="__RELABEL_FROM_FILE__" />

        <tool id="__FILTER_FROM_FILE__" />

        <tool id="__SORTLIST__" />

        <tool id="__APPLY_RULES__" />

        <tool id="__TAG_FROM_FILE__" />

        <tool id="__BUILD_LIST__" />

        <tool id="__EXTRACT_DATASET__" />

    </section>

    <section id="expression_tools" name="Expression Tools" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1" />

        <tool id="param_value_from_file" />

    </section>

    <label id="general_text_label" text="General Text Tools" version="" />

    <section id="text_manipulation" name="Text Manipulation" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.12.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.7.0+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt/1.4.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast/1.4.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase/1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.7.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.7.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.0.0" />

        <tool id="addValue" />

        <tool id="Convert characters1" />

        <tool id="cat1" />

        <tool id="Paste1" />

        <tool id="Remove beginning1" />

        <tool id="random_lines1" />

        <tool id="Show beginning1" />

        <tool id="Show tail1" />

        <tool id="trimmer" />

        <tool id="wc_gnu" />

        <tool id="secure_hash_message_digest" />

        <tool id="Condense characters1" />

        <tool id="mergeCols1" />

        <tool id="createInterval" />

        <tool id="Cut1" />

        <tool id="ChangeCase" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0" />

    </section>

    <section id="filter_and_sort" name="Filter and Sort" version="">

        <tool id="Filter1" />

        <tool id="sort1" />

        <tool id="Grep1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3" />

        <tool id="Extract_features1" />

        <tool id="gff_filter_by_attribute" />

        <tool id="gff_filter_by_feature_count" />

        <tool id="gtf_filter_by_attribute_values_list" />

        <label id="gff" text="GFF" version="" />

    </section>

    <section id="join__subtract_and_group" name="Join, Subtract and Group" version="">

        <tool id="join1" />

        <tool id="comp1" />

        <tool id="Grouping1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1" />

    </section>

    <section id="datamash" name="Datamash" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.0.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.0.6" />

    </section>

    <label id="genomic_file_manipulation_label" text="Genomic File Manipulation" version="" />

    <section id="fasta_fastq" name="FASTA/FASTQ" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.5.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/rnateam/splitfasta/rbc_splitfasta/0.4.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_concatenate_by_species/fasta_concatenate0/0.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.5" />

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    <section id="nanopore" name="Nanopore" version="">

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    <section id="convert_formats" name="Convert Formats" version="">

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    <section id="lift_over" name="Lift-Over" version="">

        <tool id="liftOver1" />

    </section>

    <label id="common_genomics_tools_label" text="Common Genomics Tools" version="" />

    <section id="interactivetools" name="Interactive tools" version="">

        <tool id="interactive_tool_jupyter_notebook" />

        <tool id="interactive_tool_rstudio" />

        <tool id="interactive_tool_panoply" />

    </section>

    <section id="operate_on_genomic_intervals" name="Operate on Genomic Intervals" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/complement/gops_complement_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/gops_basecoverage_1/1.0.0" />

        <tool id="wiggle2simple1" />

        <tool id="aggregate_scores_in_intervals2" />

        <tool id="gene2exon1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/annotation_profiler/Annotation_Profiler_0/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0" />

    </section>

    <section id="fetch_sequences_alignments" name="Fetch Sequences/Alignments" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3" />

        <tool id="Interval2Maf_pairwise1" />

        <tool id="Interval2Maf1" />

        <tool id="Interval_Maf_Merged_Fasta2" />

        <tool id="GeneBed_Maf_Fasta2" />

        <tool id="maf_stats1" />

        <tool id="MAF_Thread_For_Species1" />

        <tool id="MAF_Limit_To_Species1" />

        <tool id="maf_limit_size1" />

        <tool id="maf_by_block_number1" />

        <tool id="MAF_Reverse_Complement_1" />

        <tool id="MAF_filter" />

    </section>

    <label id="genomics_analysis_label" text="Genomics Analysis" version="" />

    <section id="assembly" name="Assembly" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.14+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/hifiasm/hifiasm/0.14" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.3.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/idba_tran/idba_tran/1.1.3+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/velvet/velvetg/1.2.10.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.3+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/miniasm/miniasm/0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.3.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/idba_ud/idba_ud/1.1.3+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/idba_tran/idba_tran/1.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/idba_hybrid/idba_hybrid/1.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nate/trinity_psc/trinity_psc/0.0.1" />

    </section>

    <section id="annotation" name="Annotation" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.14+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.0.9" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/spaln/list_spaln_tables/2.4.03+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/spaln/spaln/2.4.03+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/progressivemauve/xmfa2gff3/2015_02_13.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst_list/2.19.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst/2.19.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate_list/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tetyper/tetyper/1.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.13.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transtermhp/transtermhp/2.09.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tetyper/tetyper/1.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/0.1.7+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.6.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/spaln/spaln/2.3.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/socru/socru/2.1.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/snap_training/snap_training/2013_11_29+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.12.0+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/progressivemauve/progressivemauve/2015_02_13.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/progressivemauve/xmfa2gff3/2015_02_13.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst_list/2.16.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mlst/mlst/2.16.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/maker/maker/2.31.10+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/maker_map_ids/maker_map_ids/2.31.10" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.0.7+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_annotate/2.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_identify/2.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_orth/gprofiler_orth/0.1.7+galaxy11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_convert/gprofiler_convert/0.1.7+galaxy11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_random/gprofiler_random/0.1.7+galaxy11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_gost/gprofiler_gost/0.1.7+galaxy11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gprofiler_snpense/gprofiler_snpense/0.1.7+galaxy11" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fargene/fargene/0.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/3.0.2+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/blastxml_to_gapped_gff3/blastxml_to_gapped_gff3/1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/augustus_training/augustus_training/3.3.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.3.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.9.8" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate_list/0.9.8" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13" />

        <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0" />

    </section>

    <section id="mapping" name="Mapping" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.7a" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.5b" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.2b1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.15.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.15.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.4.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie_color_wrappers/bowtie_color_wrapper/1.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.2.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.2" />

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    <section id="variant_calling" name="Variant Calling" version="">

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/snpfreqplot/snpfreqplot/1.0+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.7.0+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/lofreq_alnqual/lofreq_alnqual/2.1.5+galaxy0" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamleftalign/bamleftalign/0.0.2" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/boris/phylorelatives/phylorelatives/0.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/boris/hetbox/hetbox/1.0" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpSift_filter/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/snpEff/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/mutate_snp_codon/mutate_snp_codon_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2" />

    </section>

    <section id="chip_seq" name="ChIP-seq" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/genrich/genrich/0.5+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/repmatch_gff3/repmatch_gff3/1.0.3" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20140616.0" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.0.20140616.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.0.20140616.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.7.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.1" />

    </section>

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.28.1.0" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.24.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.24.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.8" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.9.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.43.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.20.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.20.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8" />

        <tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.7.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.4.6.p5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.2.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.7.6.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/get_read_pipeline/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/react_cal_pipeline/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/0.0.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/0.0.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/filter_transcripts_via_tracking/filter_combined_via_tracking/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0" />

        <label id="structurefold_label" text="RNA Structure Prediction" version="" />

    </section>

    <section id="multiple_alignments" name="Multiple Alignments" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/1.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sina/sina/1.7.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/interval2maf/Interval2Maf1/1.0.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/maf_stats/maf_stats1/1.0.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/genebed_maf_to_fasta/GeneBed_Maf_Fasta2/1.0.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sina/sina/1.7.1+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/genebed_maf_to_fasta/GeneBed_Maf_Fasta2/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/maf_stats/maf_stats1/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/interval2maf/Interval2Maf1/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kc_align/kc-align/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sina/sina/1.5.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/pipelign/pipelign/0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_show_coords/mummer_show_coords/4.0.0beta2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/msaboot/msaboot/0.1.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/0.1" />

    </section>

    <section id="phenotype_association" name="Phenotype Association" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotate/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotator/0.1" />

        <tool id="hgv_codingSnps" />

        <tool id="hgv_add_scores" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ctd_batch/ctdBatch_1/1.0.0" />

        <tool id="hgv_linkToGProfile" />

        <tool id="hgv_sift" />

        <tool id="hgv_pass" />

        <tool id="hgv_gpass" />

        <tool id="hgv_ldtools" />

        <tool id="hgv_lps" />

        <tool id="hgv_david" />

        <tool id="hgv_beam" />

        <tool id="master2pgSnp" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcf2pgsnp/vcf2pgSnp/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/snpfreq/hgv_snpFreq/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/divide_pg_snp/dividePgSnp/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/hgv_fundo/hgv_funDo/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/hgv_hilbertvis/hgv_hilbertvis/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0" />

    </section>

    <section id="evolution" name="Evolution" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rapidnj/rapidnj/2.3.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tn93_readreduce/tn93_readreduce/1.0.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/tn93/tn93/1.0.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3" />

    </section>

    <section id="regional_variation" name="Regional Variation" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/windowsplitter/winSplitter/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/substitutions/substitutions1/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/weightedaverage/wtavg/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/getindels_2way/getIndels_2way/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/microsats_alignment_level/microsats_align1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/windowsplitter/winSplitter/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guru-ananda/karyotype_plot/karyotype_Plot_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guru-ananda/rhmm/hmm_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/heatmap_1/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/featurecounter/featureCoverage1/2.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/getindelrates_3way/indelRates_3way/1.0.0" />

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        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/quality_filter/qualityFilter/1.0.1" />

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    <section id="str_fm__microsatellite_analysis" name="STR-FM: Microsatellite Analysis" version="">

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    <section id="chromosome_conformation" name="Chromosome Conformation" version="">

        <label id="hifive" text="HiFive" version="" />

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    <section id="virology" name="Virology" version="">

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        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ivar_variants/ivar_variants/1.2.2+galaxy0" />

    </section>

    <label id="metagenomics_label" text="Metagenomics" version="" />

    <section id="metagenomic_analysis" name="Metagenomic Analysis" version="">

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    <section id="mothur" name="Mothur" version="">

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    </section>

    <label id="genomics_toolkits_label" text="Genomics Toolkits" version="" />

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    <section id="du_novo" name="Du Novo" version="">

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        <tool id="toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/0.7.6" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/dunovo/make_families/0.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/dunovo/align_families/0.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/dunovo/dunovo/0.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/dunovo/correct_barcodes/0.7" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/duplex/duplex/0.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/duplex/make_families/0.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/duplex/align_families/0.5" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/sequence_content_trimmer/sequence_content_trimmer/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/duplex/align_families/0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/duplex/make_families/0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/nick/duplex/duplex/0.3" />

    </section>

    <section id="seqtk" name="Seqtk" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_comp/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_randbase/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_hety/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mutfa/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_cutN/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_dropse/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_fqchk/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/1.3.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_listhet/1.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_hety/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_cutN/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_randbase/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_listhet/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_seq/1.2.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mutfa/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_dropse/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_comp/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_fqchk/1.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.2.0" />

    </section>

    <label id="miscellaneous_tools_label" text="Miscellaneous Tools" version="" />

    <section id="transposon_insertion_sequencing" name="Transposon Insertion Sequencing" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/biotradis/bacteria_tradis/1.4.5+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/biotradis/tradis_essentiality/1.4.5+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/biotradis/tradis_gene_insert_sites/1.4.5+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_resampling/transit_resampling/3.0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_hmm/transit_hmm/3.0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_tn5gaps/transit_tn5gaps/3.0.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.1+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_hmm/transit_hmm/3.0.1+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_resampling/transit_resampling/3.0.1+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_hmm/transit_hmm/3.0.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_resampling/transit_resampling/3.0.1+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_tn5gaps/transit_tn5gaps/3.0.1+galaxy2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/2.5.2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_hmm/transit_hmm/2.5.2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/2.3.3+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_hmm/transit_hmm/2.3.3+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/transit_resampling/transit_resampling/2.3.3+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/1.0.0" />

    </section>

    <section id="iwtomics" name="IWTomics" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_testandplot/iwtomics_testandplot/1.0.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_plotwithscale/iwtomics_plotwithscale/1.0.0.0" />

    </section>

    <section id="presto" name="pRESTO" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.3+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/prestor_abseq3/prestor_abseq3/0.5.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/prestor_abseq3/prestor_abseq3/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_partition/presto_partition/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_parselog/presto_parselog/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_parseheaders/presto_parseheaders/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_pairseq/presto_pairseq/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_maskprimers/presto_maskprimers/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_filterseq/presto_filterseq/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_collapseseq/presto_collapseseq/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_buildconsensus/presto_buildconsensus/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_assemblepairs/presto_assemblepairs/0.5.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/presto_alignsets/presto_alignsets/0.5.4" />

    </section>

    <section id="planttribes" name="PlantTribes" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_phylogeny_builder/plant_tribes_gene_family_phylogeny_builder/1.0.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_integrator/plant_tribes_gene_family_integrator/1.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_classifier/plant_tribes_gene_family_classifier/1.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_ks_distribution/ks_distribution/1.0.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_phylogeny_builder/plant_tribes_gene_family_phylogeny_builder/1.0.3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_integrator/plant_tribes_gene_family_integrator/1.0.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_classifier/plant_tribes_gene_family_classifier/1.0.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_gene_family_aligner/plant_tribes_gene_family_aligner/1.0.3.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_assembly_post_processor/plant_tribes_assembly_post_processor/1.0.3.0" />

    </section>

    <section id="motif" name="Motif" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/5.0.5.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/5.0.5.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_psp_gen/meme_psp_gen/5.0.5.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/weblogo3/rgweblogo3/3.5.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/weblogo3/rgweblogo3/0.4" />

    </section>

    <section id="single_cell" name="Single-cell" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.4.4.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.7.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.4+galaxy1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.2.1+2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.6.22.post1+galaxy4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.6.22.post1+galaxy4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.4.4.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.6.22.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.6.22.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/modify_loom/modify_loom/0.6.22.post1+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/3.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.2.1+galaxy6" />

    </section>

    <section id="protein_modeling" name="Protein Modeling" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_model/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_cross/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/hhsuite/hhsearch/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_map/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_model_all/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_mcc/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_minz/0.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/guerler/springsuite/spring_minz/0.1.2" />

    </section>

    <section id="proteomics" name="Proteomics" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/msstats/msstats/3.22.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/maxquant/maxquant/1.6.10.43+galaxy3" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/ident_params/1.5.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/fasta_cli/1.0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/2.0.9+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/4.0.12+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.17" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.4" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3" />

    </section>

    <section id="chemicaltoolbox" name="ChemicalToolBox" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/jmoleditor/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_pubchem_download_as_smiles/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_pubchem_download_assays/1.0.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_sdf2fps/0.1.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.2" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering/0.1" />

        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.2+galaxy0" />

        <tool id="toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0" />

    </section>

    <section id="climate_analysis" name="Climate Analysis" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/climate/ctsm_fates/ctsm_fates/2.0.1" />

    </section>

    <section id="gis_data_handling" name="GIS Data Handling" version="">

        <tool id="toolshed.g2.bx.psu.edu/repos/ecology/xarray_metadata_info/xarray_metadata_info/0.15.1" />

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    <label id="deprecated_tools_label" text="Deprecated Tools" version="" />

    <section id="genome_diversity" name="Genome Diversity" version="">

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        <label id="gd_kin" text="Kinship" version="" />

        <label id="gd_mito" text="Mitochondria" version="" />

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    <section id="cloudmap__deprecated_" name="CloudMap (deprecated)" version="">

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        <tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1" />

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    <section id="rna_analysis__deprecated_" name="RNA Analysis (deprecated)" version="">

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        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.6" />

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