Update CLI usage docs

moshi4 · Sep 14, 2024 · 315be77 · 315be77
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diff --git a/README.md b/README.md
@@ -110,6 +110,7 @@ pyMSAviz provides simple MSA visualization CLI.
 
 ### Options
 
+    $ pymsaviz --help
     usage: pymsaviz [options] -i msa.fa -o msa_viz.png
 
     MSA(Multiple Sequence Alignment) visualization CLI tool

diff --git a/docs/cli-docs/pymsaviz.md b/docs/cli-docs/pymsaviz.md
@@ -8,28 +8,33 @@
 
 ### Options
 
-    -i I, --infile I    Input MSA file
-    -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
-    --format            MSA file format (Default: 'fasta')
-    --color_scheme      Color scheme (Default: 'Zappo')
-    --start             Start position of MSA visualization (Default: 1)
-    --end               End position of MSA visualization (Default: 'MSA Length')
-    --wrap_length       Wrap length (Default: None)
-    --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
-    --label_type        Label type ('id'[default]|'description')
-    --show_grid         Show grid (Default: OFF)
-    --show_count        Show seq char count without gap on right side (Default: OFF)
-    --show_consensus    Show consensus sequence (Default: OFF)
-    --consensus_color   Consensus identity bar color (Default: '#1f77b4')
-    --consensus_size    Consensus identity bar height size (Default: 2.0)
-    --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
-    --dpi               Figure DPI (Default: 300)
-    -v, --version       Print version information
-    -h, --help          Show this help message and exit
+    $ pymsaviz --help
+    usage: pymsaviz [options] -i msa.fa -o msa_viz.png
+
+    MSA(Multiple Sequence Alignment) visualization CLI tool
+
+    optional arguments:
+      -i I, --infile I    Input MSA file
+      -o O, --outfile O   Output MSA visualization file (*.png|*.jpg|*.svg|*.pdf)
+      --format            MSA file format (Default: 'fasta')
+      --color_scheme      Color scheme (Default: 'Zappo')
+      --start             Start position of MSA visualization (Default: 1)
+      --end               End position of MSA visualization (Default: 'MSA Length')
+      --wrap_length       Wrap length (Default: None)
+      --wrap_space_size   Space size between wrap MSA plot area (Default: 3.0)
+      --label_type        Label type ('id'[default]|'description')
+      --show_grid         Show grid (Default: OFF)
+      --show_count        Show seq char count without gap on right side (Default: OFF)
+      --show_consensus    Show consensus sequence (Default: OFF)
+      --consensus_color   Consensus identity bar color (Default: '#1f77b4')
+      --consensus_size    Consensus identity bar height size (Default: 2.0)
+      --sort              Sort MSA order by NJ tree constructed from MSA distance matrix (Default: OFF)
+      --dpi               Figure DPI (Default: 300)
+      -v, --version       Print version information
+      -h, --help          Show this help message and exit
 
     Available Color Schemes:
-    ['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 
-     'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']
+    ['Clustal', 'Zappo', 'Taylor', 'Flower', 'Blossom', 'Sunset', 'Ocean', 'Hydrophobicity', 'HelixPropensity', 'StrandPropensity', 'TurnPropensity', 'BuriedIndex', 'Nucleotide', 'Purine/Pyrimidine', 'Identity', 'None']
 
 ### Example Command