diff --git a/mess/__main__.py b/mess/__main__.py index d9041b5..d1714aa 100644 --- a/mess/__main__.py +++ b/mess/__main__.py @@ -26,13 +26,13 @@ click.rich_click.SHOW_METAVARS_COLUMN = False click.rich_click.APPEND_METAVARS_HELP = True -mess_common_options = ( +cmd_common_options = ( { "name": "Common options", "options": ["--input", "--output", "--threads", "--taxonkit", "--help"], }, ) -mess_download_options = ( +cmd_dl_options = ( { "name": "Download options", "options": [ @@ -52,7 +52,7 @@ ], }, ) -mess_simulate_options = ( +cmd_sim_options = ( { "name": "Common simulators options", "options": [ @@ -98,13 +98,16 @@ ], }, ) -mess_local_sim_options = ( +local_sim_options = ( { "name": "Local genomes options", "options": ["--asm-summary", "--fasta"], }, ) +cmd_hmp_options = ({"name": "Hmp-template options", "options": ["--site", "--sample"]},) + + skip_options = ( { "name": "Skip options", @@ -129,23 +132,32 @@ mess_run = [ options - for options in mess_common_options - + mess_download_options - + mess_simulate_options + for options in cmd_common_options + + cmd_dl_options + + cmd_sim_options + skip_options + snakemake_options ] mess_download = [ - options - for options in mess_common_options + mess_download_options + snakemake_options + options for options in cmd_common_options + cmd_dl_options + snakemake_options ] mess_simulate = [ options - for options in mess_common_options - + mess_local_sim_options - + mess_simulate_options + for options in cmd_common_options + + local_sim_options + + cmd_sim_options + + skip_options + + snakemake_options +] + +hmp_options = [ + options + for options in cmd_hmp_options + + cmd_common_options + + cmd_dl_options + + cmd_sim_options + skip_options + snakemake_options ] @@ -161,9 +173,7 @@ "mess run": mess_run, "mess download": mess_download, "mess simulate": mess_simulate, - "mess hmp-template": [ - {"name": "Hmp-template options", "options": ["--site", "--sample"]} - ], + "mess hmp-template": hmp_options, } click.rich_click.COMMAND_GROUPS = { @@ -199,11 +209,11 @@ def cli(): """ \b ___ ___ _____ _____ - | \/ | / ___/ ___| - | . . | ___\ `--.\ `--. - | |\/| |/ _ \`--. \`--. \\ - | | | | __/\__/ /\__/ / - \_| |_/\___\____/\____/ + | \\/ | / ___/ ___| + | . . | ___\\ `--.\\ `--. + | |\\/| |/ _ \\`--. \\`--. \\ + | | | | __/\\__/ /\\__/ / + \\_| |_/\\___\\____/\\____/ \b For more options: @@ -232,37 +242,42 @@ def cli(): """ help_download = """ -\b +\n Downloads genomes from taxons/accessions in input table(s) -\b +\n EXAMPLES: mess download -i [input] -o [output] """ help_simulate = """ -\b +\n Simulate reads from local fasta -\b +\n EXAMPLES: mess simulate -i [input] --tech [tech] --fasta [fasta-dir] -o [output] -or +\n +or +\n mess simulate -i [input] --tech [tech] --asm-summary [asm-summary] -o [output] """ help_test = """ -\b +\n Test command to run mess from assembly download to read simulation -\b +\n EXAMPLES: mess test -o [output] """ help_hmp_templates = """ -\b +\n Command to download and simulate healthy human microbiome templates -\b +\n EXAMPLES: -mess hmp_template --site gut -o gut +\n +mess hmp-template --site gut -o gut +\n or -mess hmp_template --site buccal_mucosa --sample SRS013506 -o SRS013506 +\n +mess hmp-template --site buccal_mucosa --sample SRS013506 -o SRS013506 """