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tools_iuc.yaml
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tools_iuc.yaml
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---
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: argnorm
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: evidencemodeler
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: microsatbed
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_dada2
owner: iuc
- name: data_manager_omamer
owner: iuc
- name: data_manager_humann2_database_downloader
owner: iuc
- name: data_manager_ncbi_fcs_gx_database_downloader
owner: iuc
- name: data_manager_picard_index_builder
owner: devteam
- 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: bbgbigwig
owner: iuc
tool_panel_section_label: 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_axtchain
owner: iuc
tool_panel_section_label: Convert Formats
- name: ucsc_maftoaxt
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
- name: ucsc_nettoaxt
owner: iuc
tool_panel_section_label: Convert Formats
- name: ucsc_netfilter
owner: iuc
tool_panel_section_label: Convert Formats
- name: ucsc_chainnet
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_clipping_histogram
owner: devteam
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