usegalaxy-eu-tools/tools_iuc.yaml at master · usegalaxy-eu/usegalaxy-eu-tools · GitHub

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---
install_repository_dependencies: false
install_resolver_dependencies: false
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: angsd
    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: autobigs
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bakta
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bicodon_counts_from_fasta
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_remove_tail
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_remove_spurious_events
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_merge_pcr_duplicates
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_extract_crosslinked_nucleotides
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_extract_barcodes
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_extract_alignment_ends
    owner: iuc
    tool_panel_section_label: Annotation

  - name: bctools_convert_to_binary_barcode
    owner: iuc
    tool_panel_section_label: Annotation

  - name: busco
    owner: iuc
    tool_panel_section_label: Annotation

  - name: codon_freq_from_bicodons
    owner: iuc
    tool_panel_section_label: Annotation

  - name: colibread_takeabreak
    owner: iuc
    tool_panel_section_label: Annotation

  - name: colibread_mapsembler2
    owner: iuc
    tool_panel_section_label: Annotation

  - name: colibread_kissplice
    owner: iuc
    tool_panel_section_label: Annotation

  - name: colibread_discosnp_rad
    owner: iuc
    tool_panel_section_label: Annotation

  - name: colibread_discosnp_pp
    owner: iuc
    tool_panel_section_label: Annotation

  - name: colibread_commet
    owner: iuc
    tool_panel_section_label: Annotation

  - name: data_manager_fetch_busco_options
    owner: iuc

  - name: data_manager_bwa_mem2_index_builder
    owner: iuc

  #- name: data_manager_bwa_mem_index_builder
  #  owner: iuc

  - 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: coreprofiler_allele_calling
    owner: iuc
    tool_panel_section_label: Annotation

  - name: data_manager_build_coreprofiler
    owner: iuc

  - name: drhip
    owner: iuc
    tool_panel_section_label: Annotation

  - name: detect_circular_sequences
    owner: iuc
    tool_panel_section_label: Annotation

  - name: endorspy
    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: deeparg_predict
    owner: iuc
    tool_panel_section_label: Annotation

  - name: deeparg_short_reads
    owner: iuc
    tool_panel_section_label: Annotation

  - name: data_manager_funannotate_options
    owner: iuc

  - name: data_manager_deeparg
    owner: iuc

  - name: data_manager_fetch_plasmidfinder
    owner: iuc

  - 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: fastoma
    owner: iuc
    tool_panel_section_label: Annotation

  - name: fgsea
    owner: iuc
    tool_panel_section_label: Annotation

  - name: find_nested_alt_orfs
    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_acgt_content
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_build_icm
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_gbk_to_orf
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_extract
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_knowledge_based
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: glimmer_long_orfs
    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: hicap
    owner: iuc
    tool_panel_section_label: Annotation

  - name: hicstuff_pipeline
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mist_dists
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mist_call
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mmseqs2_easy_taxonomy
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mmseqs2_easy_search
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mmseqs2_easy_rbh
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mmseqs2_easy_linsearch
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mmseqs2_easy_cluster
    owner: iuc
    tool_panel_section_label: Annotation

  - name: psauron
    owner: iuc
    tool_panel_section_label: Annotation

  - name: neighbors
    owner: iuc
    tool_panel_section_label: Annotation

  - name: sexdeterrmine
    owner: iuc
    tool_panel_section_label: Annotation

  - name: preseq_lc_extrap
    owner: iuc
    tool_panel_section_label: "FASTQ Quality Control"

  - name: preseq_c_curve
    owner: iuc
    tool_panel_section_label: "FASTQ Quality Control"

  - name: mtnucratio
    owner: iuc
    tool_panel_section_label: "FASTQ Quality Control"

  - name: tb_profiler_profile
    owner: iuc
    tool_panel_section_label: Annotation

  - name: telogator
    owner: iuc
    tool_panel_section_label: Annotation

  - name: telescope_assign
    owner: iuc
    tool_panel_section_label: Annotation

  - name: snap
    owner: iuc
    tool_panel_section_label: Annotation

  - name: shorah_amplicon
    owner: iuc
    tool_panel_section_label: Annotation

  - name: scikit_bio_diversity_beta_diversity
    owner: iuc
    tool_panel_section_label: Annotation

  - name: remove_terminal_stop_codons
    owner: iuc
    tool_panel_section_label: Annotation

  - name: plasclass
    owner: iuc
    tool_panel_section_label: Annotation

  - name: mykrobe_predict
    owner: iuc
    tool_panel_section_label: Annotation

  - name: meningotype
    owner: iuc
    tool_panel_section_label: Annotation

  - name: longdust
    owner: iuc
    tool_panel_section_label: Annotation

  - name: liftoff
    owner: iuc
    tool_panel_section_label: Annotation

  - name: tiberius
    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: groot
    owner: iuc
    tool_panel_section_label: Annotation

  - name: data_manager_groot_database_downloader
    owner: iuc

  - 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: icescreen
    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: mmseqs2_taxonomy_assignment
    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: data_manager_sam_fasta_index_builder
    owner: devteam

  - name: optitype
    owner: iuc
    tool_panel_section_label: Annotation

  - name: orthofinder_onlygroups
    owner: iuc
    tool_panel_section_label: Annotation

  - name: pirate
    owner: iuc
    tool_panel_section_label: Annotation

  - name: panaroo
    owner: galaxy-australia
    tool_panel_section_label: Annotation

  - name: panta
    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: staramr
    owner: iuc
    tool_panel_section_label: Annotation

  - name: data_manager_build_staramr
    owner: iuc

  - 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: tb_profiler_collate
    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: ucsc_maffilter
    owner: iuc
    tool_panel_section_label: Annotation

  - name: vsnp_statistics
    owner: iuc
    tool_panel_section_label: Annotation

  - name: vsnp_get_snps
    owner: iuc
    tool_panel_section_label: Annotation

  - name: vsnp_determine_ref_from_data
    owner: iuc
    tool_panel_section_label: Annotation

  - name: vsnp_build_tables
    owner: iuc
    tool_panel_section_label: Annotation

  - name: vsnp_add_zero_coverage
    owner: iuc
    tool_panel_section_label: Annotation

  - name: windowmasker
    owner: iuc
    tool_panel_section_label: Annotation

  - name: staramr
    owner: iuc
    tool_panel_section_label: Annotation

  - name: ppanggolin_all
    owner: iuc
    tool_panel_section_label: Annotation

  - name: ppanggolin_msa
    owner: iuc
    tool_panel_section_label: Annotation

  - name: ppanggolin_projection
    owner: iuc
    tool_panel_section_label: Annotation

  - name: ppanggolin_rarefaction
    owner: iuc
    tool_panel_section_label: Annotation

  - name: ucsc_blat
    owner: yating-l
    tool_panel_section_label: Annotation

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

  - name: assembly_stats
    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: craq
    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: fastk_logex
    owner: iuc
    tool_panel_section_label: Assembly

  - name: fastk_histex
    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: hapcut2
    owner: galaxy-australia
    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: merquryfk_asmplot
    owner: iuc
    tool_panel_section_label: Assembly

  - name: merquryfk_cnplot
    owner: iuc
    tool_panel_section_label: Assembly

  - name: merquryfk_hapmaker
    owner: iuc
    tool_panel_section_label: Assembly

  - name: merquryfk_happlot
    owner: iuc
    tool_panel_section_label: Assembly

  - name: merquryfk_merquryfk
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_count_kmers
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_filter_kmers
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_histogram_kmers
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_groups_kmers
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_trio_mode
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_print
    owner: iuc
    tool_panel_section_label: Assembly

  - name: meryl_arithmetic_kmers
    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: quickmerge
    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