From 9056e1092b89d5ff4d8dbca0255a2a5c9bf1cebf Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Wed, 8 May 2024 20:30:42 +0200
Subject: [PATCH] added hmp-template options

---
 mess/__main__.py | 77 +++++++++++++++++++++++++++++-------------------
 1 file changed, 46 insertions(+), 31 deletions(-)

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
 """