tools_iuc.yaml

---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false

tools:

# ANNOTATION

  - name: abricate
    owner: iuc
    tool_panel_section_label: Annotation

  - name: abritamr
    owner: iuc
    tool_panel_section_label: Annotation

  - name: amrfinderplus
    owner: iuc
    tool_panel_section_label: Annotation

  - name: annotatemyids
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bakta
    owner: iuc
    tool_panel_section_label: Annotation

  - name: busco
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_allelecall
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_allelecallevaluator
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_createschema
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_downloadschema
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_extractcgmlst
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_joinprofiles
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_nsstats
    owner: iuc
    tool_panel_section_label: Annotation

  - name: chewbbaca_prepexternalschema
    owner: iuc
    tool_panel_section_label: Annotation

  - name: compleasm
    owner: iuc
    tool_panel_section_label: Annotation

  - name: dgidb_annotator
    owner: devteam
    tool_panel_section_label: Annotation

  - name: exonerate
    owner: iuc
    tool_panel_section_label: Annotation

  - name: fargene
    owner: iuc
    tool_panel_section_label: Annotation

  - name: fastani
    owner: iuc
    tool_panel_section_label: Annotation

  - name: fgsea
    owner: iuc
    tool_panel_section_label: Annotation

  - name: funannotate_annotate
    owner: iuc
    tool_panel_section_label: Annotation

  - name: funannotate_clean
    owner: iuc
    tool_panel_section_label: Annotation

  - name: funannotate_compare
    owner: iuc
    tool_panel_section_label: Annotation

  - name: funannotate_predict
    owner: iuc
    tool_panel_section_label: Annotation

  - name: funannotate_sort
    owner: iuc
    tool_panel_section_label: Annotation

  - name: glimmer_build_icm
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_knowledge_based
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_not_knowledge_based
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: goenrichment
    owner: iuc
    tool_panel_section_label: Annotation

  - name: tsebra
    owner: iuc
    tool_panel_section_label: Annotation

  - name: multigsea
    owner: iuc
    tool_panel_section_label: Annotation

  - name: goseq
    owner: iuc
    tool_panel_section_label: Annotation

  - name: goslimmer
    owner: iuc
    tool_panel_section_label: Annotation

  - name: gprofiler_convert
    owner: iuc
    tool_panel_section_label: Annotation

  - name: gprofiler_gost
    owner: iuc
    tool_panel_section_label: Annotation

  - name: gprofiler_orth
    owner: iuc
    tool_panel_section_label: Annotation

  - name: gprofiler_random
    owner: iuc
    tool_panel_section_label: Annotation

  - name: gprofiler_snpense
    owner: iuc
    tool_panel_section_label: Annotation

  - name: gubbins
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hamronize_summarize
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hamronize_tool
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer3
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_alimask
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmalign
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmbuild
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmconvert
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmemit
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmfetch
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmscan
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_hmmsearch
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_jackhmmer
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_nhmmer
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_nhmmscan
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hmmer_phmmer
    owner: iuc
    tool_panel_section_label: Annotation

  - name: homer_annotatepeaks
    owner: iuc
    tool_panel_section_label: Annotation

  - name: homer_findmotifs
    owner: iuc
    tool_panel_section_label: Annotation

  - name: homer_findmotifsgenome
    owner: iuc
    tool_panel_section_label: Annotation

  - name: homer_gtf_to_annotations
    owner: iuc
    tool_panel_section_label: Annotation

  - name: homer_scanmotifgenomewide
    owner: iuc
    tool_panel_section_label: Annotation

  - name: integron_finder
    owner: iuc
    tool_panel_section_label: Annotation

  - name: interproscan
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: isescan
    owner: iuc
    tool_panel_section_label: Annotation

  - name: jcvi_gff_stats
    owner: iuc
    tool_panel_section_label: Annotation

  - name: kobas
    owner: iuc
    tool_panel_section_label: Annotation

  - name: kofamscan
    owner: iuc
    tool_panel_section_label: Annotation

  - name: krocus
    owner: iuc
    tool_panel_section_label: Annotation

  - name: legsta
    owner: iuc
    tool_panel_section_label: Annotation

  - name: lorikeet_spoligotype
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mirmachine
    owner: iuc
    tool_panel_section_label: Annotation

  - name: miniprot
    owner: iuc
    tool_panel_section_label: Annotation

  - name: miniprot_index
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mitos
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mitos2
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mlst
    owner: iuc
    tool_panel_section_label: Annotation

  - name: omark
    owner: iuc
    tool_panel_section_label: Annotation

  - name: data_manager_omamer
    owner: iuc

  - name: data_manager_ncbi_fcs_gx_database_downloader
    owner: iuc

  - name: optitype
    owner: iuc
    tool_panel_section_label: Annotation

  - name: orthofinder_onlygroups
    owner: iuc
    tool_panel_section_label: Annotation

  - name: plasmidfinder
    owner: iuc
    tool_panel_section_label: Annotation

  - name: prodigal
    owner: iuc
    tool_panel_section_label: Annotation

  - name: pharokka
    owner: iuc
    tool_panel_section_label: Annotation

  - name: prokka
    owner: crs4
    tool_panel_section_label: Annotation

  - name: red
    owner: iuc
    tool_panel_section_label: Annotation

  - name: repeat_masker
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: repeatmodeler
    owner: csbl
    tool_panel_section_label: Annotation

  - name: roary
    owner: iuc
    tool_panel_section_label: Annotation

  - name: seq2hla
    owner: iuc
    tool_panel_section_label: Annotation

  - name: socru
    owner: iuc
    tool_panel_section_label: Annotation

  - name: spaln
    owner: iuc
    tool_panel_section_label: Annotation

  - name: spotyping
    owner: iuc
    tool_panel_section_label: Annotation

  - name: tb_variant_filter
    owner: iuc
    tool_panel_section_label: Annotation

  - name: tbprofiler
    owner: iuc
    tool_panel_section_label: Annotation

  - name: tbvcfreport
    owner: iuc
    tool_panel_section_label: Annotation

  - name: te_finder
    owner: iuc
    tool_panel_section_label: Annotation

  - name: tetyper
    owner: iuc
    tool_panel_section_label: Annotation

  - name: transtermhp
    owner: iuc
    tool_panel_section_label: Annotation

  - name: windowmasker
    owner: iuc
    tool_panel_section_label: Annotation

# ASSEMBLY
  - name: abyss
    owner: iuc
    tool_panel_section_label: Assembly

  - name: bellerophon
    owner: iuc
    tool_panel_section_label: Assembly

  - name: bionano_scaffold
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: biscot
    owner: iuc
    tool_panel_section_label: Assembly

  - name: colibread_lordec
    owner: iuc
    tool_panel_section_label: Assembly

  - name: disco
    owner: iuc
    tool_panel_section_label: Assembly

  - name: fastk_fastk
    owner: iuc
    tool_panel_section_label: Assembly

  - name: genomescope
    owner: iuc
    tool_panel_section_label: Assembly

  - name: getorganelle
    owner: iuc
    tool_panel_section_label: Assembly

  - name: hapog
    owner: iuc
    tool_panel_section_label: Assembly

  - name: hifiasm
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: hifiasm_meta
    owner: galaxy-australia
    tool_panel_section_label: Assembly

  - name: hypo
    owner: iuc
    tool_panel_section_label: Assembly

  - name: idba_hybrid
    owner: iuc
    tool_panel_section_label: Assembly

  - name: idba_tran
    owner: iuc
    tool_panel_section_label: Assembly

  - name: idba_ud
    owner: iuc
    tool_panel_section_label: Assembly

  - name: links
    owner: iuc
    tool_panel_section_label: Assembly

  - name: megahit
    owner: iuc
    tool_panel_section_label: Assembly

  - name: merqury
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl
    owner: iuc
    tool_panel_section_label: Assembly

  - name: metaspades
    owner: nml
    tool_panel_section_label: Assembly

  - name: minia
    owner: iuc
    tool_panel_section_label: Assembly

  - name: miniasm
    owner: iuc
    tool_panel_section_label: Assembly

  - name: mitobim
    owner: iuc
    tool_panel_section_label: Assembly

  - name: necat
    owner: iuc
    tool_panel_section_label: Assembly

  - name: novoplasty
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pairtools_dedup
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pairtools_parse
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pairtools_split
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pairtools_sort
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pairtools_stats
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pilon
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pretext_graph
    owner: iuc
    tool_panel_section_label: Assembly

  - name: pretext_map
    owner: iuc
    tool_panel_section_label: Assembly

  - name: purge_dups
    owner: iuc
    tool_panel_section_label: Assembly

  - name: quast
    owner: iuc
    tool_panel_section_label: Assembly

  - name: ragtag
    owner: iuc
    tool_panel_section_label: Assembly

  - name: raven
    owner: iuc
    tool_panel_section_label: Assembly

  - name: rnaquast
    owner: iuc
    tool_panel_section_label: Assembly

  - name: rnaspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: salsa
    owner: iuc
    tool_panel_section_label: Assembly

  - name: shasta
    owner: iuc
    tool_panel_section_label: Assembly

  - name: shovill
    owner: iuc
    tool_panel_section_label: Assembly

  - name: smudgeplot
    owner: galaxy-australia
    tool_panel_section_label: Assembly

  - name: spades
    owner: nml
    tool_panel_section_label: Assembly

  - name: spades_biosyntheticspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: spades_coronaspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: spades_metaplasmidspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: spades_metaviralspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: spades_plasmidspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: spades_rnaviralspades
    owner: iuc
    tool_panel_section_label: Assembly

  - name: trycycler_cluster
    owner: iuc
    tool_panel_section_label: Assembly

  - name: trycycler_consensus
    owner: iuc
    tool_panel_section_label: Assembly

  - name: trycycler_partition
    owner: iuc
    tool_panel_section_label: Assembly

  - name: trycycler_reconcile_msa
    owner: iuc
    tool_panel_section_label: Assembly

  - name: trycycler_subsample
    owner: iuc
    tool_panel_section_label: Assembly

  - name: unicycler
    owner: iuc
    tool_panel_section_label: Assembly

  - name: verkko
    owner: iuc
    tool_panel_section_label: Assembly

  - name: yahs
    owner: iuc
    tool_panel_section_label: Assembly


# BED

  - name: bedtools
    owner: iuc
    tool_panel_section_label: BED

  - name: bedops_sortbed
    owner: iuc
    tool_panel_section_label: BED

# COLLECTION OPERATIONS

  - name: collection_element_identifiers
    owner: iuc
    tool_panel_section_label: Collection Operations

  - name: pick_value
    owner: iuc
    tool_panel_section_label: Collection Operations

# CONVERT FORMATS

  - name: bam_to_scidx
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: bam2fastx
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: bax2bam
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: bioext_bam2msa
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: biom_convert
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: biom_add_metadata
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: biom_normalize_table
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: biom_subset_table
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: biom_summarize_table
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: biom_from_uc
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: compress_file
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: crossmap_bam
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: crossmap_bed
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: crossmap_gff
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: crossmap_region
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: crossmap_vcf
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: crossmap_wig
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: genebed_maf_to_fasta
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: gfa_to_fa
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: gffread
    owner: devteam
    tool_panel_section_label: Convert Formats

  - name: gtftobed12
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: intermine_galaxy_exchange
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: interval2maf
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: resize_coordinate_window
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: samtools_bam_to_cram
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: tooldistillator
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: tooldistillator_summarize
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: ucsc_twobittofa
    owner: iuc
    tool_panel_section_label: Convert Formats

  - name: ucsc_wigtobigwig
    owner: iuc
    tool_panel_section_label: Convert Formats

# EMBOSS

  - name: emboss_5
    owner: devteam
    tool_panel_section_label: EMBOSS


# EPIGENETICS

  - name: bwameth
    owner: iuc
    tool_panel_section_label: Mapping

  - name: moabs
    owner: iuc
    tool_panel_section_label: Epigenetics

  - name: seacr
    owner: iuc
    tool_panel_section_label: Epigenetics

  - name: vcf_filter
    owner: devteam
    tool_panel_section_label: Epigenetics


# EVOLUTION

  - name: codeml
    owner: iuc
    tool_panel_section_label: Evolution

  - name: iqtree
    owner: iuc
    tool_panel_section_label: Evolution

  - name: mutate_snp_codon
    owner: devteam
    tool_panel_section_label: Evolution

  - name: rapidnj
    owner: iuc
    tool_panel_section_label: Evolution

  - name: structure
    owner: iuc
    tool_panel_section_label: Evolution

  - name: tn93
    owner: iuc
    tool_panel_section_label: Evolution

  - name: tn93_cluster
    owner: iuc
    tool_panel_section_label: Evolution

  - name: tn93_filter
    owner: iuc
    tool_panel_section_label: Evolution

  - name: tn93_readreduce
    owner: iuc
    tool_panel_section_label: Evolution

  - name: revoluzer_crex
    owner: iuc
    tool_panel_section_label: Evolution

  - name: revoluzer_distmat
    owner: iuc
    tool_panel_section_label: Evolution

# EXPRESSION TOOLS

  - name: calculate_numeric_param
    owner: iuc
    tool_panel_section_label: Expression Tools

  - name: compose_text_param
    owner: iuc
    tool_panel_section_label: Expression Tools

  - name: map_param_value
    owner: iuc
    tool_panel_section_label: Expression Tools


# EXTRACT FEATURES

  - name: b2btools_single_sequence
    owner: iuc
    tool_panel_section_label: Extract Features

  - name: fraggenescan
    owner: iuc
    tool_panel_section_label: Extract Features

  - name: length_and_gc_content
    owner: iuc
    tool_panel_section_label: Extract Features

  - name: orfipy
    owner: iuc
    tool_panel_section_label: Extract Features

  - name: parse_mito_blast
    owner: iuc
    tool_panel_section_label: Extract Features


# FASTA/FASTQ

  - name: adapter_removal
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: art
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: bbtools_bbduk
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: bbtools_bbmerge
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: bbtools_tadpole
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: cutadapt
    owner: lparsons
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_compute_length
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_concatenate_by_species
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_filter_by_length
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_formatter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_merge_files_and_filter_unique_sequences
    owner: galaxyp
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_nucleotide_changer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_stats
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_to_tabular
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastp
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_combiner
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_filter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_groomer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_manipulation
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_masker_by_quality
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_paired_end_deinterlacer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_paired_end_interlacer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_paired_end_interlacer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_paired_end_joiner
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_paired_end_splitter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_quality_boxplot
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_quality_converter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_quality_filter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_stats
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_to_fasta
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_to_tabular
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_trimmer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastq_trimmer_by_quality
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: seqprep
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: fastqc
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastqe
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: fastqtofasta
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_artifacts_filter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_barcode_splitter
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_clipper
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_collapser
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_nucleotides_distribution
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_quality_statistics
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_renamer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_reverse_complement
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: fastx_trimmer
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: filtlong
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: flash
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: ncbi_fcs_gx
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: pear
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: rcorrector
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: seqcomplexity
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: seqkit_fx2tab
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: seqkit_locate
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: seqkit_stats
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: seqtk
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: short_reads_figure_score
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: short_reads_trim_seq
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: sickle
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: tabular_to_fasta
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: tabular_to_fastq
    owner: devteam
    tool_panel_section_label: FASTA/FASTQ

  - name: trimmomatic
    owner: pjbriggs
    tool_panel_section_label: FASTA/FASTQ

  - name: trimns
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: ucsc_fasplit
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: umi_tools_count
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: umi_tools_dedup
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: umi_tools_extract
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: umi_tools_group
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: umi_tools_whitelist
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: fasta_regex_finder
    owner: mbernt
    tool_panel_section_label: FASTA/FASTQ

  - name: rasusa
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ


# FILTER AND SORT

  - name: gffcompare
    owner: iuc
    tool_panel_section_label: Filter and Sort

  - name: xpath
    owner: iuc
    tool_panel_section_label: Filter and Sort


# GEMINI

  - name: gemini_actionable_mutations
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_amend
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_annotate
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_burden
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_db_info
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_fusions
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_gene_wise
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_inheritance
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_interactions
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_load
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_lof_sieve
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_pathways
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_qc
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_query
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_roh
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_set_somatic
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_stats
    owner: iuc
    tool_panel_section_label: Gemini

  - name: gemini_windower
    owner: iuc
    tool_panel_section_label: Gemini


# GENOME DIVERSITY

  - name: fasttree
    owner: iuc
    tool_panel_section_label: Genome Diversity


# GENOME EDITING

  - name: amplican
    owner: iuc
    tool_panel_section_label: Genome editing

  - name: crispr_studio
    owner: iuc
    tool_panel_section_label: Genome editing

  - name: sonneityping
    owner: iuc
    tool_panel_section_label: Genome editing


# GET DATA

  - name: ebi_metagenomics_run_downloader
    owner: iuc
    tool_panel_section_label: Get Data

  - name: ebi_search_rest_results
    owner: iuc
    tool_panel_section_label: Get Data

  - name: ega_download_client
    owner: iuc
    tool_panel_section_label: Get Data

  - name: gdcwebapp
    owner: iuc
    tool_panel_section_label: Get Data

  - name: iedb_api
    owner: iuc
    tool_panel_section_label: Get Data

  - name: ncbi_acc_download
    owner: iuc
    tool_panel_section_label: Get Data

  - name: ncbi_datasets
    owner: iuc
    tool_panel_section_label: Get Data

  - name: pysradb_search
    owner: iuc
    tool_panel_section_label: Get Data

  - name: sra_tools
    owner: iuc
    tool_panel_section_label: Get Data

  - name: query_impc
    owner: iuc
    tool_panel_section_label: Get Data


# GRAPH/DISPLAY DATA

  - name: geneiobio
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: bandage
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: charts
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: circos
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: fasta_nucleotide_color_plot
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ggplot2_heatmap
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ggplot2_heatmap2
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ggplot2_histogram
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ggplot2_pca
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ggplot2_point
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ggplot2_violin
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: gmaj
    owner: devteam
    tool_panel_section_label: Graph/Display Data

  - name: histogram
    owner: devteam
    tool_panel_section_label: Graph/Display Data

  - name: intervene
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: jbrowse
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: jvarkit_wgscoverageplotter
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: newick_utils
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: pathview
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: pe_histogram
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: pretext_snapshot
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: pygenometracks
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: scatterplot
    owner: devteam
    tool_panel_section_label: Graph/Display Data

  - name: tsne
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: ucsc_custom_track
    owner: devteam
    tool_panel_section_label: Graph/Display Data

  - name: volcanoplot
    owner: iuc
    tool_panel_section_label: Graph/Display Data

  - name: xy_plot
    owner: devteam
    tool_panel_section_label: Graph/Display Data


# HICEXPLORER

  - name: hicexplorer_chicaggregatestatistic
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicdifferentialtest
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicexportdata
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicplotviewpoint
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicqualitycontrol
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicsignificantinteractions
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicviewpoint
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_chicviewpointbackgroundmodel
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicadjustmatrix
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicaggregatecontacts
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicaverageregions
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicbuildmatrix
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hiccomparematrices
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hiccompartmentspolarization
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicconvertformat
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hiccorrectmatrix
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hiccorrelate
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicdetectloops
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicdifferentialtad
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicfindrestrictionsites
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicfindtads
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hichyperoptdetectloops
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicinfo
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicinterintratad
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicmergedomains
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicmergeloops
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicmergematrixbins
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicnormalize
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicpca
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicplotaverageregions
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicplotdistvscounts
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicplotmatrix
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicplotsvl
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicplotviewpoint
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicquickqc
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicsummatrices
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hictadclassifier
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hictraintadclassifier
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hictransform
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: hicexplorer_hicvalidatelocations
    owner: bgruening
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicadjustmatrix
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schiccluster
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicclustercompartments
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicclusterminhash
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicclustersvl
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicconsensusmatrices
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schiccorrectmatrices
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schiccreatebulkmatrix
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicdemultiplex
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicinfo
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicmergematrixbins
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicmergetoscool
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicnormalize
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicplotclusterprofiles
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicplotconsensusmatrices
    owner: iuc
    tool_panel_section_label: HiCExplorer

  - name: schicexplorer_schicqualitycontrol
    owner: iuc
    tool_panel_section_label: HiCExplorer


# IMAGING

  - name: idr_download_by_ids
    owner: iuc
    tool_panel_section_label: Imaging

  - name: spyboat
    owner: iuc
    tool_panel_section_label: Imaging


# JOIN, SUBTRACT AND GROUP

  - name: collection_column_join
    owner: iuc
    tool_panel_section_label: Join, Subtract and Group

  - name: subtract
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals


# MACHINE LEARNING

  - name: deepmicro
    owner: iuc
    tool_panel_section_label: Machine Learning

  - name: mcl
    owner: iuc
    tool_panel_section_label: Machine Learning

  - name: virhunter
    owner: iuc
    tool_panel_section_label: Machine Learning

  - name: decontaminator
    owner: iuc
    tool_panel_section_label: Machine Learning


# MAPPING

  - name: bbtools_bbmap
    owner: iuc
    tool_panel_section_label: Mapping

  - name: bioext_bealign
    owner: iuc
    tool_panel_section_label: Mapping

  - name: bowtie2
    owner: devteam
    tool_panel_section_label: Mapping

  - name: bowtie_color_wrappers
    owner: devteam
    tool_panel_section_label: Mapping

  - name: bowtie_wrappers
    owner: devteam
    tool_panel_section_label: Mapping

  - name: bwa
    owner: devteam
    tool_panel_section_label: Mapping

  - name: bwa_mem2
    owner: iuc
    tool_panel_section_label: Mapping

  - name: hisat2
    owner: iuc
    tool_panel_section_label: Mapping

  - name: kma
    owner: iuc
    tool_panel_section_label: Mapping

  - name: lastz
    owner: devteam
    tool_panel_section_label: Mapping

  - name: lastz_paired_reads
    owner: devteam
    tool_panel_section_label: Mapping

  - name: megablast_wrapper
    owner: devteam
    tool_panel_section_label: Mapping

  - name: megablast_xml_parser
    owner: devteam
    tool_panel_section_label: Mapping

  - name: minimap2
    owner: iuc
    tool_panel_section_label: Mapping

  - name: pbmm2
    owner: iuc
    tool_panel_section_label: Mapping

  - name: rgrnastar
    owner: iuc
    tool_panel_section_label: Mapping

  - name: rna_starsolo
    owner: iuc
    tool_panel_section_label: Mapping

  - name: star_fusion
    owner: iuc
    tool_panel_section_label: Mapping

  - name: tophat2
    owner: devteam
    tool_panel_section_label: Mapping

  - name: winnowmap
    owner: iuc
    tool_panel_section_label: Mapping


# METAGENOMIC ANALYSIS

  - name: cami_amber
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: krakentools_kreport2krona
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: krakentools_kreport2mpa
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: krakentools_beta_diversity
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: krakentools_alpha_diversity
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: krakentools_combine_kreports
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: krakentools_extract_kraken_reads
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: aldex2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_alpha_diversity
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_boxplot
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_core
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_export_fasta
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_frequency
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_heatmap
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_load
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_merge_ampvis2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_mergereplicates
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_octave
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_ordinate
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_otu_network
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_rankabundance
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_rarecurve
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_setmetadata
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_subset_samples
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_subset_taxa
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_timeseries
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ampvis2_venn
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: ancombc
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: bigscape
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: binning_refiner
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: metawrapmg_binning
    owner: galaxy-australia
    tool_panel_section_label: Metagenomic Analysis

  - name: bio_hansel
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: bracken
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: cat_add_names
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: cat_bins
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: cat_contigs
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: cat_prepare
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: cat_summarise
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_analyze
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_lineage_set
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_lineage_wf
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_plot
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_qa
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_taxon_set
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_taxonomy_wf
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_tetra
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_tree
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: checkm_tree_qa
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: concoct
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: concoct_coverage_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: concoct_cut_up_fasta
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: concoct_extract_fasta_bins
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: concoct_merge_cut_up_clustering
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: coverm_contig
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: coverm_genome
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: customize_metaphlan_database
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_assigntaxonomyaddspecies
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_dada
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_filterandtrim
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_learnerrors
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_makesequencetable
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_mergepairs
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_plotcomplexity
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_plotqualityprofile
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_removebimeradenovo
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dada2_seqcounts
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: das_tool
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: data_manager_build_bracken_database
    owner: iuc

  - name: amrfinderplus_data_manager_build
    owner: iuc

  - name: data_manager_bakta
    owner: iuc

  - name: drep_compare
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: drep_dereplicate
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dram_strainer
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dram_distill
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dram_annotate
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dram_merge_annotations
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: dram_neighborhoods
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: extract_metaphlan_database
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: fasta_to_contig2bin
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: find_diag_hits
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: gi2taxonomy
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: gtdbtk_classify_wf
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_associate
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_barplot
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_genefamilies_genus_level
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_join_tables
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_reduce_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_regroup_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_rename_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_renorm_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_rna_dna_norm
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_split_stratified_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_split_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_strain_profiler
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann2_unpack_pathways
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_associate
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_barplot
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_join_tables
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_reduce_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_regroup_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_rename_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_renorm_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_rna_dna_norm
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_split_stratified_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_split_table
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_strain_profiler
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: humann_unpack_pathways
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: instrain_compare
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: instrain_profile
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: jellyfish
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_abundance_distribution
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_abundance_distribution_single
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_count_median
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_extract_partitions
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_filter_abundance
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_filter_below_abundance_cutoff
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_normalize_by_median
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: khmer_partition
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: kleborate
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken2tax
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken_biom
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken_filter
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken_report
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken_taxonomy_report
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: kraken_translate
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: last
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: lca_wrapper
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: maaslin2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: malt_run
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: mash
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: mash_sketch
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: mapseq
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: maxbin2
    owner: mbernt
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_blast2lca
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_blast2rma
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_daa2info
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_daa2rma
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_daa_meganizer
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_read_extractor
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: megan_sam2rma
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: merge_metaphlan_tables
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: metabat2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: metabat2_jgi_summarize_bam_contig_depths
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: metaeuk_easy_predict
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: metaphlan
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: nonpareil
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: phyloseq_from_biom
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: phyloseq_from_dada2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: phyloseq_plot_ordination
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: phyloseq_plot_richness
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: plasflow
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: poisson2test
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: polypolish
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: recentrifuge
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: scoary
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: semibin
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: semibin_bin
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: semibin_concatenate_fasta
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: semibin_generate_cannot_links
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: semibin_generate_sequence_features
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: semibin_train
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: seqsero2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: srst2
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: t2ps
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: t2t_report
    owner: devteam
    tool_panel_section_label: Metagenomic Analysis

  - name: taxonomy_krona_chart
    owner: crs4
    tool_panel_section_label: Metagenomic Analysis

  - name: valet
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: vapor
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: vegan_diversity
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: vegan_fisher_alpha
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: vegan_rarefaction
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: virannot_blast2tsv
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: virannot_otu
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: virannot_rps2tsv
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: vsearch
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis

  - name: qiime_extract_viz
    owner: iuc
    tool_panel_section_label: Metagenomic Analysis


# MOTHUR

  - name: mothur_align_check
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_align_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_amova
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_anosim
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_bin_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_bellerophon
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_ccode
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_check
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_perseus
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_pintail
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_slayer
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chimera_uchime
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_chop_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_classify_otu
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_classify_rf
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_classify_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_classify_tree
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_clearcut
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_cluster
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_cluster_classic
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_cluster_fragments
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_cluster_split
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_collect_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_collect_single
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_consensus_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_cooccurrence
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_corr_axes
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_count_groups
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_count_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_create_database
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_degap_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_deunique_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_deunique_tree
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_dist_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_dist_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_fastq_info
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_filter_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_filter_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_communitytype
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_coremicrobiome
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_dists
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_group
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_groups
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_label
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_lineage
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_mimarkspackage
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_otulabels
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_otulist
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_oturep
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_otus
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_rabund
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_relabund
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_sabund
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_get_sharedseqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_hcluster
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_heatmap_bin
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_heatmap_sim
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_homova
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_indicator
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_lefse
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_libshuff
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_list_otulabels
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_list_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_biom
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_contigs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_design
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_fastq
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_group
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_lefse
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_lookup
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_make_sra
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_mantel
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_merge_files
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_merge_groups
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_merge_sfffiles
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_merge_taxsummary
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_metastats
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_mimarks_attributes
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_nmds
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_normalize_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_otu_association
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_otu_hierarchy
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_pairwise_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_parse_list
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_parsimony
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_pca
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_pcoa
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_pcr_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_phylo_diversity
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_phylotype
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_pre_cluster
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_primer_design
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_rarefaction_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_rarefaction_single
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_dists
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_groups
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_lineage
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_otulabels
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_otus
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_rare
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_remove_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_reverse_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_screen_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_sens_spec
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_seq_error
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_sffinfo
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_shhh_flows
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_shhh_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_sort_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_split_abund
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_split_groups
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_sub_sample
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_summary_qual
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_summary_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_summary_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_summary_single
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_summary_tax
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_tree_shared
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_trim_flows
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_trim_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_unifrac_unweighted
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_unifrac_weighted
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_unique_seqs
    owner: iuc
    tool_panel_section_label: Mothur

  - name: mothur_venn
    owner: iuc
    tool_panel_section_label: Mothur


# MOTIF TOOLS

  - name: meme_chip
    owner: iuc
    tool_panel_section_label: Motif Tools

  - name: meme_fimo
    owner: iuc
    tool_panel_section_label: Motif Tools

  - name: meme_meme
    owner: iuc
    tool_panel_section_label: Motif Tools

  - name: meme_psp_gen
    owner: iuc
    tool_panel_section_label: Motif Tools

  - name: weblogo3
    owner: devteam
    tool_panel_section_label: Motif Tools


# MULTIPLE ALIGNMENTS

  - name: cd_hit
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: chromeister
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: clustalw
    owner: devteam
    tool_panel_section_label: Multiple Alignments

  - name: gecko
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: kc_align
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: maf_stats
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mashmap
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: msaboot
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mummer_delta_filter
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mummer_dnadiff
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mummer_mummer
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mummer_mummerplot
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mummer_nucmer
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: mummer_show_coords
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: pipelign
    owner: iuc
    tool_panel_section_label: Multiple Alignments

  - name: sina
    owner: iuc
    tool_panel_section_label: Multiple Alignments


# NCBI BLAST

  - name: bbtools_bbduk
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: diamond
    owner: bgruening
    tool_panel_section_label: NCBI Blast

  - name: magicblast
    owner: iuc
    tool_panel_section_label: NCBI Blast

  - name: ncbi_blast_plus
    owner: devteam
    tool_panel_section_label: NCBI Blast


# NANOPORE

  - name: clair3
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: flair_collapse
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: flair_correct
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: m6anet
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: medaka_consensus
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: medaka_consensus_pipeline
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: medaka_variant
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: medaka_variant_pipeline
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: nanocompore_db
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: nanocompore_sampcomp
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: nanoplot
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: nanopolishcomp_eventaligncollapse
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: nanopolishcomp_freqmethcalculate
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: ngmlr
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: ont_fast5_api_compress_fast5
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: ont_fast5_api_fast5_subset
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: ont_fast5_api_multi_to_single_fast5
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: ont_fast5_api_single_to_multi_fast5
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: porechop
    owner: iuc
    tool_panel_section_label: Nanopore

  - name: pycoqc
    owner: iuc
    tool_panel_section_label: Nanopore


# OPERATE ON GENOMIC INTERVALS

  - name: annotation_profiler
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: basecoverage
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: cluster
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: complement
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: concat
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals


# PEAK CALLING

  - name: ccat
    owner: devteam
    tool_panel_section_label: Peak Calling

  - name: genrich
    owner: iuc
    tool_panel_section_label: Peak Calling

  - name: macs
    owner: devteam
    tool_panel_section_label: Peak Calling

  - name: macs2
    owner: iuc
    tool_panel_section_label: Peak Calling

  - name: peakzilla
    owner: iuc
    tool_panel_section_label: Peak Calling

  - name: sicer
    owner: devteam
    tool_panel_section_label: Peak Calling

  - name: zerone
    owner: iuc
    tool_panel_section_label: Peak Calling


# PHENOTYPE ASSOCIATION

  - name: ctd_batch
    owner: devteam
    tool_panel_section_label: Phenotype Association

  - name: divide_pg_snp
    owner: devteam
    tool_panel_section_label: Phenotype Association

  - name: hgv_fundo
    owner: devteam
    tool_panel_section_label: Phenotype Association

  - name: hgv_hilbertvis
    owner: devteam
    tool_panel_section_label: Phenotype Association

  - name: snpfreq
    owner: devteam
    tool_panel_section_label: Phenotype Association

  - name: vcf2pgsnp
    owner: devteam
    tool_panel_section_label: Phenotype Association


# PHYLOGENETICS

  - name: hybpiper
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_absrel
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_annotate
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_bgm
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_busted
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_cfel
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_conv
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_fade
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_fel
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_fubar
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_gard
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_meme
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_prime
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_relax
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_slac
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_sm19
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_strike_ambigs
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: hyphy_summary
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: nextalign
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: nextclade
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: pangolin
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: phyml
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_add_descriptions
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_hsp
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_metagenome_pipeline
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_pathway_pipeline
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_pipeline
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_place_seqs
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: picrust2_shuffle_predictions
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: raxml
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: sarscov2formatter
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: sarscov2summary
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: snp_dists
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: snp_sites
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: usher
    owner: iuc
    tool_panel_section_label: Phylogenetics

  - name: usher_matutils
    owner: iuc
    tool_panel_section_label: Phylogenetics


# PICARD

  - name: picard
    owner: devteam
    tool_panel_section_label: Picard


# PROTEOMICS

  - name: prot_scriber
    owner: iuc
    tool_panel_section_label: Proteomics

  - name: proteinortho
    owner: iuc
    tool_panel_section_label: Proteomics

  - name: proteinortho_grab_proteins
    owner: iuc
    tool_panel_section_label: Proteomics

  - name: proteinortho_summary
    owner: iuc
    tool_panel_section_label: Proteomics

  - name: syndiva
    owner: iuc
    tool_panel_section_label: Proteomics


# QUALITY CONTROL

  - name: multiqc
    owner: iuc
    tool_panel_section_label: Quality Control


# RAD-SEQ

  - name: bayescan
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_assembleperead
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_cstacks
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_denovomap
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_genotypes
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_populations
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_procrad
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_pstacks
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_refmap
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_rxstacks
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_sstacks
    owner: iuc
    tool_panel_section_label: RAD-seq

  - name: stacks_ustacks
    owner: iuc
    tool_panel_section_label: RAD-seq


# RNA ANALYSIS

  - name: arriba
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: arriba_draw_fusions
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: arriba_get_filters
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: barrnap
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: cemitool
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: cherri_eval
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: cherri_train
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: chira_collapse
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: chira_extract
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: chira_map
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: chira_merge
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: chira_quantify
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: circexplorer2
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: crosscontamination_barcode_filter
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: cuffcompare
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cuffdiff
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cufflinks
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cuffmerge
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cuffnorm
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cuffquant
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cummerbund
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: cummerbund_to_tabular
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: deg_annotate
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: deseq2
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: dexseq
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: edger
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: egsea
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: express
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: featurecounts
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: feelnc
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: filter_transcripts_via_tracking
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: genomic_super_signature
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: heinz
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: htseq_count
    owner: lparsons
    tool_panel_section_label: RNA Analysis

  - name: idr
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: isoformswitchanalyzer
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: kallisto_pseudo
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: kallisto_quant
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: limma_voom
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: masigpro
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: migmap
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: mirnature
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: qualimap_counts
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: qualimap_rnaseq
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: ribowaltz_plot
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: ribowaltz_process
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: rnaquast
    owner: iuc
    tool_panel_section_label: Assembly

  - name: rseqc
    owner: nilesh
    tool_panel_section_label: RNA Analysis

  - name: ruvseq
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: sailfish
    owner: bgruening
    tool_panel_section_label: RNA Analysis

  - name: salmon
    owner: bgruening
    tool_panel_section_label: RNA Analysis

  - name: salmonquantmerge
    owner: bgruening
    tool_panel_section_label: RNA Analysis

  - name: scpipe
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: seurat
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: sleuth
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: slamdunk
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: sleuth
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: stringtie
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: tetoolkit_tetranscripts
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: tophat_fusion_post
    owner: devteam
    tool_panel_section_label: RNA Analysis

  - name: transdecoder
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_abundance_estimates_to_matrix
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_align_and_estimate_abundance
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_contig_exn50_statistic
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_filter_low_expr_transcripts
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_gene_to_trans_map
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_run_de_analysis
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_super_transcripts
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinity_stats
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: trinotate
    owner: iuc
    tool_panel_section_label: RNA Analysis

  - name: tximport
    owner: iuc
    tool_panel_section_label: RNA Analysis


# REGIONAL VARIATION

  - name: categorize_elements_satisfying_criteria
    owner: devteam
    tool_panel_section_label: Regional Variation

  - name: compute_motif_frequencies_for_all_motifs
    owner: devteam
    tool_panel_section_label: Regional Variation

  - name: compute_motifs_frequency
    owner: devteam
    tool_panel_section_label: Regional Variation

  - name: delete_overlapping_indels
    owner: devteam
    tool_panel_section_label: Regional Variation

  - name: draw_stacked_barplots
    owner: devteam
    tool_panel_section_label: Graph/Display Data

  - name: featurecounter
    owner: devteam
    tool_panel_section_label: Regional Variation

  - name: indels_3way
    owner: devteam
    tool_panel_section_label: Regional Variation


# SAM/BAM

  - name: bamtools
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: bamtools_filter
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: bamtools_split
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: bamtools_split_mapped
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: bamtools_split_paired
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: bamtools_split_ref
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: bamtools_split_tag
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: bamutil_diff
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: ngsutils_bam_filter
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: pileup_interval
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: pileup_parser
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: qualimap_bamqc
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: qualimap_multi_bamqc
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: sam2interval
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: sam_merge
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: sam_pileup
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtool_filter2
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_ampliconclip
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_bedcov
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_calmd
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_coverage
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_depth
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_fastx
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_fixmate
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_flagstat
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_idxstats
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_markdup
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_merge
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: samtools_mpileup
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_phase
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_reheader
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_rmdup
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_slice_bam
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_sort
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_split
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_stats
    owner: devteam
    tool_panel_section_label: SAM/BAM

  - name: samtools_view
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: tag_pileup_frequency
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: mosdepth
    owner: iuc
    tool_panel_section_label: SAM/BAM

  - name: tasmanian_mismatch
    owner: iuc
    tool_panel_section_label: SAM/BAM

# SANGER SEQUENCING

  - name: tracy_align
    owner: iuc
    tool_panel_section_label: Sanger Sequencing

  - name: tracy_assemble
    owner: iuc
    tool_panel_section_label: Sanger Sequencing

  - name: tracy_basecall
    owner: iuc
    tool_panel_section_label: Sanger Sequencing

  - name: tracy_decompose
    owner: iuc
    tool_panel_section_label: Sanger Sequencing


# SEND DATA

  - name: ena_upload
    owner: iuc
    tool_panel_section_label: Send Data


# SINGLE-CELL

  - name: sceasy_convert
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: velocyto_cli
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: cite_seq_count
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: alevin
    owner: bgruening
    tool_panel_section_label: Single-cell

  - name: anndata_export
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: anndata_import
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: anndata_inspect
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: anndata_manipulate
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: dropletutils
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: modify_loom
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: raceid_clustering
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: raceid_filtnormconf
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: raceid_inspectclusters
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: raceid_inspecttrajectory
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: raceid_trajectory
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scanpy_cluster_reduce_dimension
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scanpy_filter
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scanpy_inspect
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scanpy_normalize
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scanpy_plot
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scanpy_remove_confounders
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_create_qcmetric_ready_sce
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_filter
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_normalize
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_plot_dist_scatter
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_plot_exprs_freq
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_plot_pca
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: scater_plot_tsne
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: sinto_barcode
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: sinto_fragments
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: episcanpy_build_matrix
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: episcanpy_preprocess
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: episcanpy_cluster_embed
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: baredsc_1d
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: baredsc_2d
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: baredsc_combine_1d
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: baredsc_combine_2d
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: snapatac2_preprocessing
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: snapatac2_clustering
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: snapatac2_plotting
    owner: iuc
    tool_panel_section_label: Single-cell

  - name: snapatac2_peaks_and_motif
    owner: iuc
    tool_panel_section_label: Single-cell

# STATISTICS

  - name: best_regression_subsets
    owner: devteam
    tool_panel_section_label: Statistics

  - name: canonical_correlation_analysis
    owner: devteam
    tool_panel_section_label: Statistics

  - name: correlation
    owner: devteam
    tool_panel_section_label: Statistics

  - name: count_gff_features
    owner: devteam
    tool_panel_section_label: Statistics

  - name: dwt_var_perfeature
    owner: devteam
    tool_panel_section_label: Statistics

  - name: generate_pc_lda_matrix
    owner: devteam
    tool_panel_section_label: Statistics

  - name: graphembed
    owner: iuc
    tool_panel_section_label: Statistics

    ## IWtomic - Interval-Wise Testing for Omics Data

  - name: iwtomics_loadandplot
    owner: iuc
    tool_panel_section_label: Statistics

  - name: iwtomics_plotwithscale
    owner: iuc
    tool_panel_section_label: Statistics

  - name: iwtomics_testandplot
    owner: iuc
    tool_panel_section_label: Statistics

  - name: kernel_canonical_correlation_analysis
    owner: devteam
    tool_panel_section_label: Statistics

  - name: kernel_principal_component_analysis
    owner: devteam
    tool_panel_section_label: Statistics

  - name: lda_analysis
    owner: devteam
    tool_panel_section_label: Statistics

  - name: mine
    owner: devteam
    tool_panel_section_label: Statistics

  - name: plot_from_lda
    owner: devteam
    tool_panel_section_label: Statistics

  - name: principal_component_analysis
    owner: devteam
    tool_panel_section_label: Statistics

  - name: rgcca
    owner: iuc
    tool_panel_section_label: Statistics

  - name: t_test_two_samples
    owner: devteam
    tool_panel_section_label: Statistics


# TEXT MANIPULATION

  - name: add_value
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: basecoverage
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: cluster
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: column_maker
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: column_order_header_sort
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: column_remove_by_header
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: coverage
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: dna_filtering
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: filter_tabular
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: flanking_features
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: get_flanks
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: gff3_rebase
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: intersect
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: join
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: jq
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: merge
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: merge_cols
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: metagenomeseq_normalization
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: prinseq
    owner: iuc
    tool_panel_section_label: FASTA/FASTQ

  - name: query_tabular
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: reshape2_cast
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: reshape2_melt
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: subtract
    owner: devteam
    tool_panel_section_label: Operate on Genomic Intervals

  - name: subtract_query
    owner: devteam
    tool_panel_section_label: Text Manipulation

  - name: table_compute
    owner: iuc
    tool_panel_section_label: Text Manipulation

  - name: tables_arithmetic_operations
    owner: devteam
    tool_panel_section_label: Text Manipulation


# VARIANT CALLING

  - name: artic_guppyplex
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: artic_minion
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bamleftalign
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: basil
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bbtools_callvariants
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_annotate
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_call
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_cnv
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_concat
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_consensus
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_convert_from_vcf
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_convert_to_vcf
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_csq
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_filter
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_gtcheck
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_isec
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_merge
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_mpileup
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_norm
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_plugin_color_chrs
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_plugin_frameshifts
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_plugin_setgt
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_plugin_split_vep
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_query
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_reheader
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_roh
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_stats
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: bcftools_view
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: beacon2_csv2xlsx
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: beacon2_pxf2bff
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: beacon2_vcf2bff
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: beagle
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: breseq
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnv_phenopacket
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnv_vcf2json
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_access
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_antitarget
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_autobin
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_batch
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_breaks
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_call
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_coverage
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_diagram
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_fix
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_genemetrics
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_heatmap
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_reference
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_scatter
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_segment
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_segmetrics
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_sex
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cnvkit_target
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: control_freec
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: cutesv
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: deepvariant
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: delly_call
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: delly_classify
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: delly_cnv
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: delly_filter
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: delly_lr
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: delly_merge
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: ensembl_vep
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: freebayes
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: gatk4_mutect2
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: get_hrun
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: irissv
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: jasminesv
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: king
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lofreq_alnqual
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lofreq_call
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lofreq_filter
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lofreq_indelqual
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lofreq_viterbi
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lumpy_prep
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: lumpy_sv
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: mixcr_analyze
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: ococo
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: odgi_build
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: odgi_viz
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: plink
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: sansa_annotate
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: seqwish
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: smgu_frameshift_deletions_checks
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: sniffles
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snippy
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snpeff
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snpeff_sars_cov_2
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snpsift
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snpsift_dbnsfp
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snpsift_dbnsfp_generic
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: snpsift_genesets
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: strelka_germline
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: strelka_somatic
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: ucsc_fatovcf
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vardict_java
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: variant_analyzer
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: varscan_copynumber
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: varscan_mpileup
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: varscan_somatic
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vcf2maf
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vcf2tsv
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfaddinfo
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfallelicprimitives
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfanno
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vcfannotate
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfannotategenotypes
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfbedintersect
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfbreakcreatemulti
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfcheck
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfcombine
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfcommonsamples
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfdistance
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfdistance
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vcffilter
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcffixup
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfflatten
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfgeno2haplo
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfgenotypes
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfhethom
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfleftalign
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfprimers
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfrandomsample
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfselectsamples
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfsort
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcftools_annotate
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcftools_compare
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcftools_isec
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcftools_merge
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcftools_slice
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcftools_subset
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vcfvcfintersect
    owner: devteam
    tool_panel_section_label: Variant Calling

  - name: vg_convert
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vg_deconstruct
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vg_view
    owner: iuc
    tool_panel_section_label: Variant Calling

  - name: vt_variant_tools
    owner: iuc
    tool_panel_section_label: Variant Calling


# VIROLOGY

  - name: cooc_mutbamscan
    owner: iuc
    tool_panel_section_label: Virology

  - name: cooc_pubmut
    owner: iuc
    tool_panel_section_label: Virology

  - name: cooc_tabmut
    owner: iuc
    tool_panel_section_label: Virology

  - name: freyja_aggregate_plot
    owner: iuc
    tool_panel_section_label: Virology

  - name: freyja_boot
    owner: iuc
    tool_panel_section_label: Virology

  - name: freyja_demix
    owner: iuc
    tool_panel_section_label: Virology

  - name: freyja_variants
    owner: iuc
    tool_panel_section_label: Virology

  - name: lineagespot
    owner: iuc
    tool_panel_section_label: Virology

  - name: ivar_consensus
    owner: iuc
    tool_panel_section_label: Virology

  - name: ivar_filtervariants
    owner: iuc
    tool_panel_section_label: Virology

  - name: ivar_getmasked
    owner: iuc
    tool_panel_section_label: Virology

  - name: ivar_removereads
    owner: iuc
    tool_panel_section_label: Virology

  - name: ivar_trim
    owner: iuc
    tool_panel_section_label: Virology

  - name: ivar_variants
    owner: iuc
    tool_panel_section_label: Virology

  - name: read_it_and_keep
    owner: iuc
    tool_panel_section_label: Virology

  - name: snipit
    owner: iuc
    tool_panel_section_label: Virology

  - name: snpfreqplot
    owner: iuc
    tool_panel_section_label: Virology

  - name: varvamp
    owner: iuc
    tool_panel_section_label: Virology

  #- name: virheat
  #  owner: iuc
  #  tool_panel_section_label: Virology


# DATA MANAGERS

  - name: data_manager_build_kraken2_database
    owner: iuc

  - name: data_manager_diamond_database_builder
    owner: iuc

  - name: data_manager_funannotate
    owner: iuc

  - name: data_manager_genomic_super_signature_ravmodels
    owner: iuc

  - name: data_manager_humann_database_downloader
    owner: iuc

  - name: data_manager_interproscan
    owner: iuc

  - name: data_manager_malt_index_builder
    owner: iuc

  - name: data_manager_metaphlan_database_downloader
    owner: iuc

  - name: data_manager_nextclade
    owner: iuc

  - name: data_manager_pangolin_data
    owner: iuc

  - name: data_manager_primer_scheme_bedfiles
    owner: iuc

  - name: data_manager_semibin
    owner: iuc

  - name: data_manager_vep_cache_downloader
    owner: iuc

  - name: data_manager_pharokka
    owner: iuc

  - name: data_manager_mapseq
    owner: iuc

  - name: data_manager_gtdbtk_database_installer
    owner: iuc


# DEEPTOOLS

  - name: deeptools_alignmentsieve
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_bam_compare
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_bam_coverage
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_bam_pe_fragmentsize
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_bigwig_compare
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_compute_gc_bias
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_compute_matrix
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_compute_matrix_operations
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_correct_gc_bias
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_estimatereadfiltering
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_multi_bam_summary
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_multi_bigwig_summary
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_correlation
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_coverage
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_enrichment
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_fingerprint
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_heatmap
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_pca
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_plot_profile
    owner: bgruening
    tool_panel_section_label: deepTools

  - name: deeptools_bigwig_average
    owner: bgruening
    tool_panel_section_label: deepTools


# EXTRACT_GENOMIC_DNA

  - name: extract_genomic_dna
    owner: iuc
    tool_panel_section_id: fetch_sequences___alignments


# METABOLOMICS
  - name: mzmine_batch
    owner: iuc
    tool_panel_section_label: Metabolomics

# METABOLOMICS DIMET

  - name: dimet_abundance_plot
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_differential_analysis
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_differential_multigroup_analysis
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_enrichment_plot
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_isotopologues_plot
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_metabologram
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_pca_analysis
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_pca_plot
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_timecourse_analysis
    owner: iuc
    tool_panel_section_label: Metabolomics

  - name: dimet_bivariate_analysis
    owner: iuc
    tool_panel_section_label: Metabolomics

# METABOLOMICS TRACEGROOMER

  - name: tracegroomer
    owner: iuc
    tool_panel_section_label: Metabolomics