From 125289960f0d2868df822958c1c4c2182ed13101 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A1t=C3=A9=20Balajti?= Date: Fri, 15 Nov 2024 08:29:25 +0100 Subject: [PATCH] update guides --- docs/guides/usage.rst | 62 ++++++++++++++++++++++++------------------- docs/index.rst | 4 +-- 2 files changed, 36 insertions(+), 30 deletions(-) diff --git a/docs/guides/usage.rst b/docs/guides/usage.rst index 15b25ce..d7525b9 100644 --- a/docs/guides/usage.rst +++ b/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. | diff --git a/docs/index.rst b/docs/index.rst index b623fad..1b241c6 100644 --- a/docs/index.rst +++ b/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: