Merge pull request #7 from DOED-DAAD/dev

updated cli parser options

README.md

@@ -38,11 +38,60 @@ hatch run +py=3.10 test:mikrokondo-tools
 
 The above command will display command groups with help messages, and each sub command has additional help options.
 
-Console installation has not been tested.
 ```console
 pip install mikrokondo-tools
 ```
 
+## Usage
+
+Running `mikrokondo-tools` generates the following help message with available options for usage:
+
+```
+Usage: mikrokondo-tools [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --version   Show the version and exit.
+  -h, --help  Show this message and exit.
+
+Commands:
+  download     Download a database for mikrokondo
+  samplesheet  Generate a sample sheet for mikrokondo.
+```
+
+The `download` option generates the following output:
+
+```
+Usage: mikrokondo-tools download [OPTIONS]
+
+  Download a external file for use in mikrokondo. This script only downloads
+  the file and will not untar or unzip them.
+
+Options:
+  -f, --file [gtdb-sketch|gtdb-shigella|dehost|kraken-std|bakta-light|bakta-full]
+                                  Pick an option from the list to download
+                                  [required]
+  -o, --output PATH               An existing directory to download files to.
+                                  [default: your/current/directory]
+  -h, --help                      Show this message and exit.
+```
+
+
+The `samplesheet` option produces the following output:
+
+```
+Usage: mikrokondo-tools samplesheet [OPTIONS] SAMPLE_DIRECTORY
+
+Options:
+  -o, --output-sheet PATH   The file to write your created output sheet to,
+                            this directory must already exist.  [required]
+  -1, --read-1-suffix TEXT  A suffix to identify read 1  [default: _R1_]
+  -2, --read-2-suffix TEXT  A suffix to identify read 2  [default: _R2_]
+  -s, --schema-input PATH   An optional schema_input.json file pre-downloaded
+                            for mikrokondo.
+  -h, --help                Show this message and exit.
+```
+
+
 ## License
 
 Copyright Government of Canada 2023

src/mikrokondo_tools/cli/download/__init__.py

@@ -5,15 +5,16 @@
 from mikrokondo_tools.download import download as dwnld
 
 options = {"gtdb-sketch": dwnld.Constants.sketch_url,
+        "gtdb-shigella": dwnld.Constants.shigella_sketch,
         "dehost": dwnld.Constants.dehost_idx,
         "kraken-std": dwnld.Constants.kraken2_std,
         "bakta-light": dwnld.Constants.bakta_light,
         "bakta-full": dwnld.Constants.bakta_full}
 
-@click.command(short_help="Download a database for mikrokondo", no_args_is_help=True)
+@click.command(short_help="Download a database for mikrokondo", no_args_is_help=True, context_settings={'show_default': True})
 @click.option("-f", "--file", "file", type=click.Choice(options.keys()), required = True,
             help="Pick an option from the list to download")
-@click.option("-o", "--output", "output", default=os.getcwd(), type=click.Path(), help="An existing directory to download files too.")
+@click.option("-o", "--output", "output", default=os.getcwd(), type=click.Path(), help="An existing directory to download files to.")
 def download(file, output):
     """Download a external file for use in mikrokondo. This script only downloads the file and will not untar or unzip them.
     """

src/mikrokondo_tools/cli/samplesheet/__init__.py

@@ -6,7 +6,7 @@
 from mikrokondo_tools.samplesheet import samplesheet as ss
 import mikrokondo_tools.utils as u
 
-@click.command(short_help="Generate a sample sheet for mikrokondo.", no_args_is_help=True)
+@click.command(short_help="Generate a sample sheet for mikrokondo.", no_args_is_help=True, context_settings={'show_default': True})
 @click.option("-o", "--output-sheet", "output_sheet", required=True, type=click.Path(), help="The file to write your created output sheet to, this directory must already exist.")
 @click.option("-1", "--read-1-suffix", "read_1", type=click.STRING, help="A suffix to identify read 1", default="_R1_")
 @click.option("-2", "--read-2-suffix", "read_2", type=click.STRING, help="A suffix to identify read 2", default="_R2_")

src/mikrokondo_tools/download/download.py

@@ -18,6 +18,7 @@
 @dataclass(frozen=True)
 class Constants:
     sketch_url: str = "https://zenodo.org/records/8408361/files/GTDBSketch_20231003.msh"
+    shigella_sketch: str = "https://zenodo.org/records/13969103/files/EnteroRef_GTDBSketch_20231003_V2.msh"
     dehost_idx: str = "https://zenodo.org/records/8408557/files/PhiPacHum_m2.idx"
     kraken2_std: str = "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240112.tar.gz"
     bakta_light: str = "https://zenodo.org/records/10522951/files/db-light.tar.gz"

tests/download/test_download.py

@@ -26,6 +26,8 @@ def test_constants_connection(uri):
 @pytest.mark.parametrize( "input_url,value",
                         [("https://zenodo.org/records/8408361/files/GTDBSketch_20231003.msh",
                         "GTDBSketch_20231003.msh"),
+                        ("https://zenodo.org/records/13969103/files/EnteroRef_GTDBSketch_20231003_V2.msh",
+                        "EnteroRef_GTDBSketch_20231003_V2.msh"),
                         ("https://zenodo.org/records/8408557/files/PhiPacHum_m2.idx",
                         "PhiPacHum_m2.idx"),
                         ("https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240112.tar.gz",