update help message

Author: shenwei356

docs/content/usage/index/_index.md

@@ -114,7 +114,7 @@ Important parameters:
                             ($input_files / --batch-size), please increase this value and set a bigger "ulimit -n" in shell.
 
 Usage:
-  lexicmap index [flags] [-k <k>] [-m <masks>] { -I <seqs dir> | -X <file list>} -O <out dir>
+  lexicmap index [flags] [-k <k>] [-m <masks>] {-I <seqs dir> | [-S] -X <file list>} -O <index.lmi>
 
 Flags:
   -b, --batch-size int            ► Maximum number of genomes in each batch (maximum value: 131072)

docs/content/usage/search.md

@@ -70,7 +70,7 @@ Result ordering:
   3. Results of multiple subject genomes are sorted by the highest SimilarityScore of HSP clusters.
 
 Usage:
-  lexicmap search [flags] -d <index path> [query.fasta.gz ...] [-o query.tsv.gz]
+  lexicmap search [flags] -d <index path> [query.fasta[.gz] ...] [-o result.tsv[.gz]]
 
 Flags:
       --align-band int                 ► Band size in backtracking the score matrix (pseudo alignment

lexicmap/cmd/index.go

@@ -615,7 +615,7 @@ func init() {
 	indexCmd.Flags().BoolP("debug", "", false,
 		formatFlagUsage(`Print debug information.`))
 
-	indexCmd.SetUsageTemplate(usageTemplate("[-k <k>] [-m <masks>] { -I <seqs dir> | -X <file list>} -O <out dir>"))
+	indexCmd.SetUsageTemplate(usageTemplate("[-k <k>] [-m <masks>] {-I <seqs dir> | [-S] -X <file list>} -O <index.lmi>"))
 }
 
 var defaultChunks int

lexicmap/cmd/search.go

@@ -757,7 +757,7 @@ func init() {
 	mapCmd.Flags().BoolP("debug", "", false,
 		formatFlagUsage(`Print debug information, including a progress bar. (recommended when searching with one query).`))
 
-	mapCmd.SetUsageTemplate(usageTemplate("-d <index path> [query.fasta.gz ...] [-o query.tsv.gz]"))
+	mapCmd.SetUsageTemplate(usageTemplate("-d <index path> [query.fasta[.gz] ...] [-o result.tsv[.gz]]"))
 
 	// filter by taxids