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asaim.yaml
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asaim.yaml
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---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false
tools:
# data_retrieval
- name: 'suite_ebi_tools'
owner: 'iuc'
tool_panel_section_label: 'Get Data'
- name: 'suite_enasearch'
owner: 'iuc'
tool_panel_section_label: 'Get Data'
- name: 'suite_ncbi_entrez'
owner: 'iuc'
tool_panel_section_label: 'Get Data'
- name: 'sra_tools'
owner: 'iuc'
tool_panel_section_label: 'Get Data'
# quality_control
- name: 'fastqc'
owner: 'devteam'
tool_panel_section_label: 'Quality Control'
- name: 'prinseq'
owner: 'iuc'
tool_panel_section_label: 'Quality Control'
- name: 'trim_galore'
owner: 'bgruening'
tool_panel_section_label: 'Quality Control'
- name: 'trimmomatic'
owner: 'pjbriggs'
tool_panel_section_label: 'Quality Control'
- name: 'multiqc'
owner: 'iuc'
tool_panel_section_label: 'Quality Control'
# clustering
- name: 'cdhit'
owner: 'bebatut'
tool_panel_section_label: 'Multiple Alignments'
- 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 analyses'
- name: 'nonpareil'
owner: 'iuc'
tool_panel_section_label: 'Metagenomic analyses'
# 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: 'valet'
owner: 'iuc'
tool_panel_section_label: 'Metagenomic analyses'
# amplicon_sequence_processing
- name: 'suite_mothur'
owner: 'iuc'
tool_panel_section_label: 'mothur'
- name: 'suite_qiime'
owner: 'iuc'
tool_panel_section_label: 'Qiime'
- name: 'data_manager_qiime_database_downloader'
owner: 'iuc'
tool_panel_section_label: Data Managers
# wgs_taxonomic_assignations
- name: 'suite_metaphlan2'
owner: 'iuc'
tool_panel_section_label: 'Metagenomic analyses'
- name: 'format_metaphlan2_output'
owner: 'bebatut'
tool_panel_section_label: 'Metagenomic analyses'
- name: 'suite_kraken_0_10_5'
owner: 'devteam'
tool_panel_section_label: 'Metagenomic analyses'
# metabolism_assignation
- name: 'suite_humann2'
owner: 'iuc'
tool_panel_section_label: 'Metagenomic analyses'
- name: 'group_humann2_uniref_abundances_to_go'
owner: 'bebatut'
tool_panel_section_label: 'Metagenomic analyses'
- name: 'compare_humann2_output'
owner: 'bebatut'
tool_panel_section_label: 'Metagenomic analyses'
- name: 'interproscan5'
owner: 'bgruening'
tool_panel_section_label: 'Metagenomic analyses'
- name: 'suite_picrust'
owner: 'iuc'
tool_panel_section_label: 'Annotation'
# combination_taxo_func
- name: 'combine_metaphlan2_humann2'
owner: 'bebatut'
tool_panel_section_label: 'Metagenomic analyses'
# visualization
- name: 'export2graphlan'
owner: 'iuc'
tool_panel_section_label: 'Graph/Display Data'
- name: 'suite_graphlan'
owner: 'iuc'
tool_panel_section_label: 'Graph/Display Data'
- name: 'taxonomy_krona_chart'
owner: 'crs4'
tool_panel_section_label: 'Graph/Display Data'