update guides

docs/guides/usage.rst

@@ -35,37 +35,43 @@ Command-line Options
 
 Available command-line parameters are categorized as follows:
 
-- **General Options**:
-    - :code:`--output-directory`: Path where output data will be saved.
-    - :code:`--temporary-directory`: Path for storing temporary files generated during execution.
-    - :code:`--cleanup-regime`: Specifies which data should be kept after completion. Available options are :code:`DEFAULT`, :code:`KEEP_ALL`, :code:`KEEP_NONE`, and :code:`KEEP_RESULTS`.
-    - :code:`--verbosity`: Controls the verbosity level of log output; options are :code:`DEBUG`, :code:`INFO`, :code:`WARN`, :code:`ERROR`, and :code:`CRITICAL`.
+.. table:: General Options
+    :widths: 25, 75
 
-- **Library-specific Options**:
-    - :code:`PATH [PATH]`: Path(s) to the RNA-Seq input data. For paired-end libraries, provide paths to both mate files. 
-    - :code:`--transcripts`: Path to the FASTA file containing transcript sequences for reference.
-    - :code:`--read-layout-adapters`: Path to a file with 3' adapter sequences (one sequence per line) used to identify adapter content.
-    - :code:`--read-layout-min-match-percentage`: Minimum percentage of reads containing an adapter for it to be considered as the library’s 3’-end adapter.
-    - :code:`--read-layout-min-frequency-ratio`: Minimum frequency ratio between the most and second most frequent adapters to select the 3’-end adapter.
-    - :code:`--library-source-min-match-percentage`: Minimum percentage of reads aligning with a library source for it to be considered representative of the library.
-    - :code:`--library-source-min-frequency-ratio`: Minimum frequency ratio between primary and secondary library sources, ensuring only the most prominent source is identified.
-    - :code:`--library-type-max-distance`: Maximum allowable distance between read pairs to classify the library type.
-    - :code:`--library-type-mates-cutoff`: Ratio cutoff to determine the consistency of mate orientation in paired-end reads.
-    - :code:`--read-orientation-min-mapped-reads`: Minimum number of mapped reads to ensure reliable inference of read orientation.
-    - :code:`--read-orientation-min-fraction`: Minimum fraction (must exceed 0.5) of reads supporting a given orientation to confirm its accuracy.
+.. table:: General Options
+   :widths: 25, 75
 
-- **Processing and Performance Options**:
-    - :code:`--records`: Limits the number of input records to process; setting this to 0 will process all records.
-    - :code:`--threads`: Specifies the number of threads for concurrent processing to optimize performance.
-    - :code:`--tax-id`: Taxonomy ID for the sample source, aiding in organism-specific analyses.
+   | Option | Description |
+   |---|---|
+   | :code:`--output-directory PATH` | Path where output data will be saved. |
+   | :code:`--temporary-directory PATH` | Path for storing temporary files generated during execution. |
+   | :code:`--cleanup-regime {DEFAULT,KEEP_ALL,KEEP_NONE,KEEP_RESULTS}` | Specifies which data should be kept after completion. |
+   | :code:`--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}` | Controls the verbosity level of log output. |
+   | :code:`-h, --help` | Show help screen and exit. |
+   | :code:`--version` | Show version information and exit. |
 
-Meta Options
-------------
+.. table:: Library-specific Options
+   :widths: 25, 75
 
-For help or version information, use the following:
+   | Option | Description |
+   |---|---|
+   | `PATH [PATH]` | Path(s) to the RNA-Seq input data. For paired-end libraries, provide paths to both mate files. |
+   | `--transcripts FASTA` | Path to the FASTA file containing transcript sequences for reference. |
+   | `--read-layout-adapters PATH` | Path to a file with 3' adapter sequences (one sequence per line) used to identify adapter content. |
+   | `--read-layout-min-match-percentage FLOAT` | Minimum percentage of reads containing an adapter for it to be considered as the library’s 3’-end adapter. |
+   | `--read-layout-min-frequency-ratio FLOAT` | Minimum frequency ratio between the most and second most frequent adapters to select the 3’-end adapter. |
+   | `--library-source-min-match-percentage FLOAT` | Minimum percentage of reads aligning with a library source for it to be considered representative of the library. |
+   | `--library-source-min-frequency-ratio FLOAT` | Minimum frequency ratio between primary and secondary library sources, ensuring only the most prominent source is identified. |
+   | `--library-type-max-distance INT` | Maximum allowable distance between read pairs to classify the library type. |
+   | `--library-type-mates-cutoff FLOAT` | Ratio cutoff to determine the consistency of mate orientation in paired-end reads. |
+   | `--read-orientation-min-mapped-reads INT` | Minimum number of mapped reads to ensure reliable inference of read orientation. |
+   | `--read-orientation-min-fraction FLOAT` | Minimum fraction (must exceed 0.5) of reads supporting a given orientation to confirm its accuracy. |
 
-.. code-block:: bash
-
-   htsinfer --help
-   htsinfer --version
+.. table:: Processing and Performance Options
+   :widths: 25, 75
 
+   | Option | Description |
+   |---|---|
+   | `--records INT` | Limits the number of input records to process; setting this to 0 will process all records. |
+   | `--threads INT` | Specifies the number of threads for concurrent processing to optimize performance. |
+   | `--tax-id INT` | Taxonomy ID for the sample source, aiding in organism-specific analyses. |

docs/index.rst

@@ -6,9 +6,9 @@
 Welcome to the HTSinfer documentation pages!
 ============================================
 
-`HTSinfer` is a command-line tool that infers metadata from Illumina high-throughput sequencing (HTS) data. 
+`HTSinfer` is a command-line tool that infers RNA-Seq metadata from Illumina high-throughput sequencing (HTS) data. 
 
-This documentation will guide you through installation, usage, and the API reference.
+This documentation will guide you through installation and usage. It also contains an API reference.
 
 .. toctree::
    :hidden: