Config File Details

Config File Details

Required input

This workflow has the following required inputs and their description:

• "aces.datadb": "/path/to/database_file"
• "aces.samples_file": "/path/to/list_of_genomes.txt",
• "aces.threshold": Query Length Percentage Threshold, as a float (0.3)
• "aces.query": "/path/to/query.fa",
• "aces.pathToInput": "/path/to/database",
• "aces.eval": BLAST evalue threshold, as a float (0.00001)

Optional input

Here are all of the optional commands. To include them locally, copy the option into your inputs.json file (i.e "aces.<option_name>":), and fill in the corresponding value. If you don't want to include them, don't add it to inputs.json. In the cloud, you just need to fill in the corresponding value in the input table.

The commands are divided into non-BLAST and BLAST related options. Commands with #BLAST next to them are BLAST or dc-megablast specific options. You can find more information about each BLAST command in the documentation found here:

non-BLAST

• "aces.raxmlHPC_model_type": "String? (optional)", #Model type for RAxML
• "aces.msa_threads": "Int? (optional)", #Number of CPUs to use in the MSA/RAxML step
• "aces.num_bootstraps": "Int? (optional)", #Number of bootstraps for RAxML to run
• "aces.blast_ram": "Int? (optional)", #Amount of RAM to run the BLAST job
• "aces.num_threads_blast": "Int? (optional)",
• "aces.msa_ram": "Int? (optional)", #Amount of RAM to use in the MSA/RAxML step

BLAST

• "aces.num_threads_blast": "Int? (optional)", #Number of threads to use with BLAST
• "aces.lcase_masking": "String? (optional)", #BLAST
• "aces.word_size": "Int? (optional)", #BLAST
• "aces.filtering_db": "Array[File]? (optional)", #BLAST
• "aces.query_loc": "String? (optional)", #BLAST
• "aces.soft_masking": "String? (optional)", #BLAST
• "aces.best_hit_overhang": "Float? (optional)", #BLAST
• "aces.best_hit_score_edge": "Float? (optional)", #BLAST
• "aces.culling_limit": "Int? (optional)", #BLAST
• "aces.penalty": "Int? (optional)", #BLAST
• "aces.min_raw_gapped_score": "Int? (optional)", #BLAST
• "aces.searchsp": "Int? (optional)", #BLAST
• "aces.window_size": "Int? (optional)", #BLAST
• "aces.show_gis": "String? (optional)", #BLAST
• "aces.dust": "String? (optional)", #BLAST
• "aces.gapextend": "Int? (optional)", #BLAST
• "aces.mt_mode": "Int? (optional)", #BLAST
• "aces.xdrop_ungap": "Int? (optional)", #BLAST
• "aces.xdrop_gap": "Int? (optional)", #BLAST
• "aces.reward": "Int? (optional)", #BLAST
• "aces.max_num_seq": "Int? (optional)", #BLAST
• "aces.template_length": "Int? (optional)", #BLAST
• "aces.perc_identity": "Int? (optional)", #BLAST
• "aces.template_type": "String? (optional)", #BLAST
• "aces.dbsize": "Int? (optional)", #BLAST
• "aces.ungapped": "String? (optional)", #BLAST
• "aces.parse_deflines": "String? (optional)", #BLAST
• "aces.gapopen": "Int? (optional)", #BLAST
• "aces.import_search_strategy": "File? (optional)", #BLAST
• "aces.export_search_strategy": "String? (optional)", #BLAST
• "aces.max_hsps": "Int? (optional)", #BLAST
• "aces.strand": "String? (optional)", #BLAST
• "aces.xdrop_gap_final": "Int? (optional)", #BLAST
• "aces.filtering_db_path": "String? (optional)" #BLAST