asaim.yaml

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

tools:

    # data_retrieval
  - name: 'sra_tools'
    owner: 'iuc'
    tool_panel_section_label: 'Get Data'

    # quality_control
  - name: 'fastqc'
    owner: 'devteam'
    tool_panel_section_label: "FASTA/FASTQ"

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

  - name: 'trim_galore'
    owner: 'bgruening'
    tool_panel_section_label: "FASTA/FASTQ"

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

  - name: 'multiqc'
    owner: 'iuc'
    tool_panel_section_label: Quality Control

    # clustering

  - name: 'format_cd_hit_output'
    owner: 'bebatut'
    tool_panel_section_label: 'Multiple Alignments'

    # sorting
  - name: 'sortmerna'
    owner: 'rnateam'
    tool_panel_section_label: 'Annotation'

  - name: 'data_manager_sortmerna_database_downloader'
    owner: 'rnateam'
    tool_panel_section_label: Data Managers

    # similarity_search
  - name: 'ncbi_blast_plus'
    owner: 'devteam'
    tool_panel_section_label: 'NCBI Blast'

  - name: 'diamond'
    owner: 'bgruening'
    tool_panel_section_label: 'NCBI Blast'

    # mapping
  - name: 'bwa'
    owner: 'devteam'
    tool_panel_section_label: 'Mapping'

  - name: 'bowtie2'
    owner: 'devteam'
    tool_panel_section_label: 'Mapping'

    # alignment
  - name: 'hmmer3'
    owner: 'iuc'
    tool_panel_section_label: 'Annotation'

    # metagenomics_manipulation
  - name: 'vsearch'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic Analysis'
  - name: 'nonpareil'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic Analysis'

    # assembly
  - name: 'megahit'
    owner: 'iuc'
    tool_panel_section_label: 'Assembly'

  - name: 'metaspades'
    owner: 'nml'
    tool_panel_section_label: 'Assembly'

  - name: 'quast'
    owner: 'iuc'
    tool_panel_section_label: 'Assembly'

  - name: 'refseq_masher'
    owner: 'nml'
    tool_panel_section_label: 'Assembly'   

  - name: 'valet'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic Analysis'

    # amplicon_sequence_processing

  - name: 'data_manager_qiime_database_downloader'
    owner: 'iuc'
    tool_panel_section_label: Data Managers

    # wgs_taxonomic_assignations

  - name: 'format_metaphlan2_output'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic Analysis'

    # metabolism_assignation

  - name: 'group_humann2_uniref_abundances_to_go'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic Analysis'

  - name: 'compare_humann2_output'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic Analysis'

  - name: 'interproscan5'
    owner: 'bgruening'
    tool_panel_section_label: 'Annotation'

    # combination_taxo_func
  - name: 'combine_metaphlan2_humann2'
    owner: 'bebatut'
    tool_panel_section_label: 'Metagenomic Analysis'

    # visualization
  - name: 'export2graphlan'
    owner: 'iuc'
    tool_panel_section_label: 'Graph/Display Data'


  - name: 'taxonomy_krona_chart'
    owner: 'crs4'
    tool_panel_section_label: 'Metagenomic Analysis'

    # AMR
  - name: 'kleborate'
    owner: 'iuc'
    tool_panel_section_label: 'Metagenomic Analysis'