idc/data_managers.yml at main · galaxyproject/idc · GitHub

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data_manager_fetch_genome_dbkeys_all_fasta:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.4'
  tags:
    - fetch_source
data_manager_bowtie2_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.3.4.3'
  tags:
    - genome
data_manager_bwa_mem_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.3'
  tags:
    - genome
  parameters:
    index_algorithm: bwtsw
data_manager_hisat_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_hisat_index_builder/hisat_index_builder_data_manager/1.0.0'
  tags:
    - genome
data_manager_twobit_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/twobit_builder_data_manager/0.0.2'
  tags:
    - genome
data_manager_picard_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/picard_index_builder_data_manager/2.7.1'
  tags:
    - genome
data_manager_sam_fasta_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2'
  tags:
    - genome
data_manager_hisat2_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/hisat2_index_builder_data_manager/2.0.5'
  tags:
    - genome
data_manager_star_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/rna_star_index_builder_data_manager/2.7.4a+galaxy1'
  tags:
    - genome
data_manager_bowtie_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/bowtie_color_space_index_builder_data_manager/0.0.2'
  tags:
    - genome
data_manager_kallisto_index_builder:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_kallisto_index_builder/kallisto_index_builder_data_manager/0.43.1'
  tags:
    - genome
data_manager_snpeff:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager_snpeff_databases/4.3r'
  tags:
    - snpeff
data_manager_plant_tribes_scaffolds_downloader:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_plant_tribes_scaffolds_downloader/data_manager_plant_tribes_scaffolds_download/1.1.0'
  tags:
    - plant_source
data_manager_fetch_ncbi_taxonomy:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_ncbi_taxonomy/ncbi_taxonomy_fetcher/1.0.0'
  tags:
    - tax_source
data_manager_gemini_database_downloader:
  tool_id: 'toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.20.1'
  tags:
    - gemini
data_manager_build_kraken2_database:
  tool_id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_build_kraken2_database/kraken2_build_database/2.1.2+galaxy1
  tags:
    - kraken2
data_manager_build_bracken_database:
  tool_id: toolshed.g2.bx.psu.edu/repos/iuc/data_manager_build_bracken_database/bracken_build_database/2.8+galaxy0
  parameters:
    kraken_db: "{{ item.id }}"
    check_prebuilt:
      prebuilt: yes
  tags:
    - bracken