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tools_iuc.yaml
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---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false
tools:
- name: bedtools
owner: iuc
tool_panel_section_label: Operate on Genomic Intervals
- name: collection_element_identifiers
owner: iuc
tool_panel_section_label: Collection Operations
- name: crosscontamination_barcode_filter
owner: iuc
tool_panel_section_label: RNA Analysis
- name: deg_annotate
owner: iuc
tool_panel_section_label: RNA Analysis
- name: raceid_inspectclusters
owner: iuc
tool_panel_section_label: RNA Analysis
- name: raceid_filtnormconf
owner: iuc
tool_panel_section_label: RNA Analysis
- name: raceid_clustering
owner: iuc
tool_panel_section_label: RNA Analysis
- name: raceid_trajectory
owner: iuc
tool_panel_section_label: RNA Analysis
- name: raceid_inspecttrajectory
owner: iuc
tool_panel_section_label: RNA Analysis
- name: kallisto_quant
owner: iuc
tool_panel_section_label: RNA Analysis
- name: slamdunk
owner: iuc
tool_panel_section_label: RNA Analysis
- name: plasflow
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: ruvseq
owner: iuc
tool_panel_section_label: RNA Analysis
- name: kallisto_pseudo
owner: iuc
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: feelnc
owner: iuc
tool_panel_section_label: RNA Analysis
- name: volcanoplot
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: nanoplot
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: intervene
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: charts
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ggplot2_pca
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: pygenometracks
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ggplot2_heatmap
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ggplot2_violin
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ggplot2_heatmap2
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ggplot2_point
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ggplot2_histogram
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: tsne
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: idr
owner: iuc
tool_panel_section_label: RNA Analysis
- name: circos
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ebi_search_rest_results
owner: iuc
tool_panel_section_label: Get Data
- name: ebi_metagenomics_run_downloader
owner: iuc
tool_panel_section_label: Get Data
- name: column_maker
owner: devteam
tool_panel_section_label: Text Manipulation
- name: reshape2_melt
owner: iuc
tool_panel_section_label: Text Manipulation
- name: reshape2_cast
owner: iuc
tool_panel_section_label: Text Manipulation
- name: sra_tools
owner: iuc
tool_panel_section_label: Get Data
- name: codeml
owner: iuc
tool_panel_section_label: Evolution
- name: prinseq
owner: iuc
tool_panel_section_label: Text Manipulation
- name: add_value
owner: devteam
tool_panel_section_label: Text Manipulation
- name: dwt_var_perfeature
owner: devteam
tool_panel_section_label: Statistics
- name: merge_cols
owner: devteam
tool_panel_section_label: Text Manipulation
- name: jq
owner: iuc
tool_panel_section_label: Text Manipulation
- name: column_maker
owner: devteam
tool_panel_section_label: Text Manipulation
- name: coverage
owner: devteam
tool_panel_section_label: Text Manipulation
- name: tables_arithmetic_operations
owner: devteam
tool_panel_section_label: Text Manipulation
- name: merge
owner: devteam
tool_panel_section_label: Text Manipulation
- name: intersect
owner: devteam
tool_panel_section_label: Text Manipulation
- name: flanking_features
owner: devteam
tool_panel_section_label: Text Manipulation
- name: join
owner: devteam
tool_panel_section_label: Text Manipulation
- name: cluster
owner: devteam
tool_panel_section_label: Text Manipulation
- name: get_flanks
owner: devteam
tool_panel_section_label: Text Manipulation
- name: complement
owner: devteam
tool_panel_section_label: Text Manipulation
- name: subtract
owner: devteam
tool_panel_section_label: Text Manipulation
- name: basecoverage
owner: devteam
tool_panel_section_label: Text Manipulation
- name: subtract_query
owner: devteam
tool_panel_section_label: Text Manipulation
- name: dna_filtering
owner: devteam
tool_panel_section_label: Text Manipulation
- name: collection_column_join
owner: iuc
tool_panel_section_label: Join, Subtract and Group
- name: suite_datamash
owner: iuc
tool_panel_section_label: Join, Subtract and Group
- name: subtract
owner: devteam
tool_panel_section_label: Join, Subtract and Group
- name: bam_to_scidx
owner: iuc
tool_panel_section_label: Convert Formats
- name: resize_coordinate_window
owner: iuc
tool_panel_section_label: Convert Formats
- name: gffread
owner: devteam
tool_panel_section_label: Convert Formats
- name: ucsc_twobittofa
owner: iuc
tool_panel_section_label: Convert Formats
- name: tabular_to_fasta
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: filtlong
owner: iuc
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_to_tabular
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastqtofasta
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_to_fasta
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastp
owner: iuc
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_stats
owner: iuc
tool_panel_section_label: FASTA/FASTQ manipulation
- name: length_and_gc_content
owner: iuc
tool_panel_section_label: Extract Features
- name: extract_genomic_dna
owner: iuc
tool_panel_section_label: Other Tools
- name: concat
owner: devteam
tool_panel_section_label: Operate on Genomic Intervals
- name: complement
owner: devteam
tool_panel_section_label: Operate on Genomic Intervals
- name: cluster
owner: devteam
tool_panel_section_label: Operate on Genomic Intervals
- name: basecoverage
owner: devteam
tool_panel_section_label: Operate on Genomic Intervals
- name: annotation_profiler
owner: devteam
tool_panel_section_label: Operate on Genomic Intervals
- name: t_test_two_samples
owner: devteam
tool_panel_section_label: Statistics
- name: plot_from_lda
owner: devteam
tool_panel_section_label: Statistics
- name: mine
owner: devteam
tool_panel_section_label: Statistics
- name: lda_analysis
owner: devteam
tool_panel_section_label: Statistics
- name: generate_pc_lda_matrix
owner: devteam
tool_panel_section_label: Statistics
- name: count_gff_features
owner: devteam
tool_panel_section_label: Statistics
- name: correlation
owner: devteam
tool_panel_section_label: Statistics
- name: fasta_nucleotide_color_plot
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: jbrowse
owner: iuc
tool_panel_section_label: Graph/Display Data
- name: ucsc_custom_track
owner: devteam
tool_panel_section_label: Graph/Display Data
- name: scatterplot
owner: devteam
tool_panel_section_label: Graph/Display Data
- name: histogram
owner: devteam
tool_panel_section_label: Graph/Display Data
- name: gmaj
owner: devteam
tool_panel_section_label: Graph/Display Data
- name: xy_plot
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
- name: draw_stacked_barplots
owner: devteam
tool_panel_section_label: Regional Variation
- name: delete_overlapping_indels
owner: devteam
tool_panel_section_label: Regional Variation
- name: compute_motifs_frequency
owner: devteam
tool_panel_section_label: Regional Variation
- name: compute_motif_frequencies_for_all_motifs
owner: devteam
tool_panel_section_label: Regional Variation
- name: categorize_elements_satisfying_criteria
owner: devteam
tool_panel_section_label: Regional Variation
- name: best_regression_subsets
owner: devteam
tool_panel_section_label: Statistics
- name: principal_component_analysis
owner: devteam
tool_panel_section_label: Statistics
- name: kernel_principal_component_analysis
owner: devteam
tool_panel_section_label: Statistics
- name: kernel_canonical_correlation_analysis
owner: devteam
tool_panel_section_label: Statistics
- name: canonical_correlation_analysis
owner: devteam
tool_panel_section_label: Statistics
- name: mutate_snp_codon
owner: devteam
tool_panel_section_label: Evolution
- name: iqtree
owner: iuc
tool_panel_section_label: Evolution
- name: structure
owner: iuc
tool_panel_section_label: Evolution
- name: meme_meme
owner: iuc
tool_panel_section_label: Motif Tools
- name: meme_fimo
owner: iuc
tool_panel_section_label: Motif Tools
- name: meme_psp_gen
owner: iuc
tool_panel_section_label: Motif Tools
- name: meme_chip
owner: iuc
tool_panel_section_label: Motif Tools
- name: weblogo3
owner: devteam
tool_panel_section_label: Motif Tools
- name: mummer_mummer
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: mummer_show_coords
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: mummer_dnadiff
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: mummer_nucmer
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: mummer_delta_filter
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: mummer_mummerplot
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: msaboot
owner: iuc
tool_panel_section_label: Multiple Alignments
- name: clustalw
owner: devteam
tool_panel_section_label: Multiple Alignments
- name: bio_hansel
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: vegan_diversity
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: vegan_fisher_alpha
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: vegan_rarefaction
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: vsearch
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_filter_abundance
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_filter_below_abundance_cutoff
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_extract_partitions
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_abundance_distribution
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_count_median
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_partition
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_normalize_by_median
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: khmer_abundance_distribution_single
owner: iuc
tool_panel_section_label: Metagenomic analyses
- name: t2t_report
owner: devteam
tool_panel_section_label: Metagenomic analyses
- name: t2ps
owner: devteam
tool_panel_section_label: Metagenomic analyses
- name: poisson2test
owner: devteam
tool_panel_section_label: Metagenomic analyses
- name: lca_wrapper
owner: devteam
tool_panel_section_label: Metagenomic analyses
- name: gi2taxonomy
owner: devteam
tool_panel_section_label: Metagenomic analyses
- name: find_diag_hits
owner: devteam
tool_panel_section_label: Metagenomic analyses
- name: fasta_merge_files_and_filter_unique_sequences
owner: galaxyp
tool_panel_section_label: FASTA/FASTQ manipulation
- name: sickle
owner: iuc
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_paired_end_interlacer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_paired_end_joiner
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_compute_length
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: pear
owner: iuc
tool_panel_section_label: FASTA/FASTQ manipulation
- name: flash
owner: iuc
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_artifacts_filter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_barcode_splitter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_clipper
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_nucleotides_distribution
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_filter_by_length
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_concatenate_by_species
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_collapser
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_nucleotide_changer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fasta_formatter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastqc
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_paired_end_joiner
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: short_reads_trim_seq
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: short_reads_figure_score
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: tabular_to_fastq
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_trimmer_by_quality
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_trimmer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_to_tabular
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_stats
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_paired_end_splitter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_paired_end_interlacer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_paired_end_deinterlacer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_masker_by_quality
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_manipulation
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_groomer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_filter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_combiner
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_trimmer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_reverse_complement
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_renamer
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastx_quality_statistics
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_quality_filter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_quality_converter
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: fastq_quality_boxplot
owner: devteam
tool_panel_section_label: FASTA/FASTQ manipulation
- name: shovill
owner: iuc
tool_panel_section_label: Assembly
- name: idba_ud
owner: iuc
tool_panel_section_label: Assembly
- name: megahit
owner: iuc
tool_panel_section_label: Assembly
- name: rnaspades
owner: iuc
tool_panel_section_label: Assembly
- name: unicycler
owner: iuc
tool_panel_section_label: Assembly
- name: pilon
owner: iuc
tool_panel_section_label: Assembly
- name: quast
owner: iuc
tool_panel_section_label: Assembly
- name: tophat2
owner: devteam
tool_panel_section_label: Mapping
- name: bowtie2
owner: devteam
tool_panel_section_label: Mapping
- name: rgrnastar
owner: iuc
tool_panel_section_label: Mapping
- name: star_fusion
owner: iuc
tool_panel_section_label: Mapping
- name: hisat2
owner: iuc
tool_panel_section_label: Mapping
- name: bowtie_wrappers
owner: devteam
tool_panel_section_label: Mapping
- name: bowtie_color_wrappers
owner: devteam
tool_panel_section_label: Mapping
- name: bwa
owner: devteam
tool_panel_section_label: Mapping
- name: megablast_xml_parser
owner: devteam
tool_panel_section_label: Mapping
- name: megablast_wrapper
owner: devteam
tool_panel_section_label: Mapping
- name: lastz_paired_reads
owner: devteam
tool_panel_section_label: Mapping
- name: lastz
owner: devteam
tool_panel_section_label: Mapping
- name: minimap2
owner: iuc
tool_panel_section_label: Mapping
- name: migmap
owner: iuc
tool_panel_section_label: RNA Analysis
- name: sailfish
owner: bgruening
tool_panel_section_label: RNA Analysis
- name: deseq2
owner: iuc
tool_panel_section_label: RNA Analysis
- name: edger
owner: iuc
tool_panel_section_label: RNA Analysis
- name: limma_voom
owner: iuc
tool_panel_section_label: RNA Analysis
- name: salmon
owner: bgruening
tool_panel_section_label: RNA Analysis
- name: featurecounts
owner: iuc
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_super_transcripts
owner: iuc
tool_panel_section_label: RNA Analysis
- name: trinity_align_and_estimate_abundance
owner: iuc
tool_panel_section_label: RNA Analysis
- name: trinity_abundance_estimates_to_matrix
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_run_de_analysis
owner: iuc
tool_panel_section_label: RNA Analysis
- name: suite_trinity
owner: iuc
tool_panel_section_label: RNA Analysis
- name: tophat_fusion_post
owner: devteam
tool_panel_section_label: RNA Analysis
- name: stringtie
owner: iuc
tool_panel_section_label: RNA Analysis
- name: dexseq
owner: iuc
tool_panel_section_label: RNA Analysis
- name: cuffdiff
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cummerbund_to_tabular
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cummerbund
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cuffmerge
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cuffquant
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cuffnorm
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cuffcompare
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cufflinks
owner: devteam
tool_panel_section_label: RNA Analysis
- name: filter_transcripts_via_tracking
owner: devteam
tool_panel_section_label: RNA Analysis
- name: express
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cufflinks
owner: devteam
tool_panel_section_label: RNA Analysis
- name: cuffcompare
owner: devteam
tool_panel_section_label: RNA Analysis
- name: masigpro
owner: iuc
tool_panel_section_label: RNA Analysis
- name: macs2
owner: iuc
tool_panel_section_label: Peak Calling
- name: macs
owner: devteam
tool_panel_section_label: Peak Calling
- name: zerone
owner: iuc
tool_panel_section_label: Peak Calling
- name: sicer
owner: devteam
tool_panel_section_label: Peak Calling
- name: ccat
owner: devteam
tool_panel_section_label: Peak Calling
- name: bwameth
owner: iuc
tool_panel_section_label: Epigenetics
- name: vcf_filter
owner: devteam
tool_panel_section_label: Epigenetics
- name: varscan_mpileup
owner: iuc
tool_panel_section_label: Variant Calling
- name: varscan_somatic
owner: iuc
tool_panel_section_label: Variant Calling
- name: varscan_copynumber
owner: iuc
tool_panel_section_label: Variant Calling
- name: suite_varscan
owner: iuc
tool_panel_section_label: Variant Calling
- name: freebayes
owner: devteam
tool_panel_section_label: Variant Calling
- name: ococo
owner: iuc
tool_panel_section_label: Variant Calling
- name: snippy
owner: iuc
tool_panel_section_label: Variant Calling
- name: vcf2pgsnp
owner: devteam
tool_panel_section_label: Phenotype Association
- name: snpfreq
owner: devteam
tool_panel_section_label: Phenotype Association
- name: hgv_hilbertvis
owner: devteam
tool_panel_section_label: Phenotype Association
- name: hgv_fundo
owner: devteam
tool_panel_section_label: Phenotype Association
- name: divide_pg_snp
owner: devteam
tool_panel_section_label: Phenotype Association
- name: ctd_batch
owner: devteam
tool_panel_section_label: Phenotype Association
- name: goenrichment
owner: iuc
tool_panel_section_label: Annotation
- name: goslimmer
owner: iuc
tool_panel_section_label: Annotation
- name: goseq
owner: iuc
tool_panel_section_label: Annotation
- name: fgsea
owner: iuc
tool_panel_section_label: Annotation
- name: egsea
owner: iuc
tool_panel_section_label: RNA Analysis
- name: kobas