Updated the cli

artic-network · Sep 10, 2024 · 943f9b7 · 943f9b7
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diff --git a/README.md b/README.md
@@ -310,39 +310,37 @@ Create a new scheme in the required format
 **Usage**:
 
 ```console
-$ primal-page create [OPTIONS] SCHEMEPATH
+$ primal-page create [OPTIONS]
 ```
 
-**Arguments**:
-
-* `SCHEMEPATH`: The path to the primerscheme directory  [required]
-
 **Options**:
 
 * `--schemename TEXT`: The name of the scheme  [required]
 * `--ampliconsize INTEGER RANGE`: Amplicon size  [x>=100; required]
 * `--schemeversion TEXT`: Scheme version, default is parsed from config.json  [required]
 * `--species INTEGER`: The species this scheme targets. Please use NCBI taxonomy ids  [required]
 * `--authors TEXT`: Any authors  [required]
+* `--primerbed PATH`: The path to the primer.bed file  [required]
+* `--reference PATH`: The path to the reference.fasta file  [required]
 * `--schemestatus [withdrawn|deprecated|autogenerated|draft|tested|validated]`: Scheme status  [default: draft]
 * `--citations TEXT`: Any associated citations. Please use DOI
-* `--primerbed PATH`: Manually specify the primer bed file, default is *primer.bed
-* `--reference PATH`: Manually specify the reference.fasta file, default is *.fasta
 * `--output PATH`: Where to output the scheme  [default: primerschemes]
 * `--configpath PATH`: Where the config.json file is located
 * `--algorithmversion TEXT`: The version of primalscheme or other
 * `--description TEXT`: A description of the scheme
 * `--derivedfrom TEXT`: Which scheme has this scheme been derived from
 * `--primerclass [primerschemes]`: The primer class  [default: primerschemes]
-* `--collection [ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET]`: The collection
+* `--collection [ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP]`: The collection
 * `--link-protocol TEXT`: Optional link to protocol
 * `--link-validation TEXT`: Optional link to validation data
 * `--links-homepage TEXT`: Optional link to homepage
 * `--link-vendor TEXT`: Optional link to vendors
 * `--link-misc TEXT`: Optional miscellaneous link
 * `--fix / --no-fix`: Attempt to fix the scheme  [default: no-fix]
-* `--help`: Show this message and exit.
 * `--contact-info TEXT`: Contact information
+* `--additional-files PATH`: Additional files to include in the ./work directory
+* `--help`: Show this message and exit.
+
 
 ## `primal-page download`
 
@@ -480,13 +478,13 @@ Add a Collection to the Collection list in the info.json file
 **Usage**:
 
 ```console
-$ primal-page modify add-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}
+$ primal-page modify add-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}
 ```
 
 **Arguments**:
 
 * `SCHEMEINFO`: The path to info.json  [required]
-* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}`: The Collection to add  [required]
+* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}`: The Collection to add  [required]
 
 **Options**:
 
@@ -689,13 +687,13 @@ Remove an Collection from the Collection list in the info.json file
 **Usage**:
 
 ```console
-$ primal-page modify remove-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}
+$ primal-page modify remove-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}
 ```
 
 **Arguments**:
 
 * `SCHEMEINFO`: The path to info.json  [required]
-* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}`: The Collection to remove  [required]
+* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}`: The Collection to remove  [required]
 
 **Options**:
 
@@ -756,4 +754,4 @@ $ primal-page remove [OPTIONS] SCHEMEINFO
 
 **Options**:
 
-* `--help`: Show this message and exit.
+* `--help`: Show this message and exit.
diff --git a/docs/assets/primal-page-create.png b/docs/assets/primal-page-create.png
diff --git a/docs/cli.md b/docs/cli.md
@@ -107,39 +107,38 @@ Create a new scheme in the required format
 **Usage**:
 
 ```console
-$ primal-page create [OPTIONS] SCHEMEPATH
+$ primal-page create [OPTIONS]
 ```
 
-**Arguments**:
-
-* `SCHEMEPATH`: The path to the primerscheme directory  [required]
-
 **Options**:
 
 * `--schemename TEXT`: The name of the scheme  [required]
 * `--ampliconsize INTEGER RANGE`: Amplicon size  [x>=100; required]
 * `--schemeversion TEXT`: Scheme version, default is parsed from config.json  [required]
 * `--species INTEGER`: The species this scheme targets. Please use NCBI taxonomy ids  [required]
 * `--authors TEXT`: Any authors  [required]
+* `--primerbed PATH`: The path to the primer.bed file  [required]
+* `--reference PATH`: The path to the reference.fasta file  [required]
 * `--schemestatus [withdrawn|deprecated|autogenerated|draft|tested|validated]`: Scheme status  [default: draft]
 * `--citations TEXT`: Any associated citations. Please use DOI
-* `--primerbed PATH`: Manually specify the primer bed file, default is *primer.bed
-* `--reference PATH`: Manually specify the reference.fasta file, default is *.fasta
 * `--output PATH`: Where to output the scheme  [default: primerschemes]
 * `--configpath PATH`: Where the config.json file is located
 * `--algorithmversion TEXT`: The version of primalscheme or other
 * `--description TEXT`: A description of the scheme
 * `--derivedfrom TEXT`: Which scheme has this scheme been derived from
 * `--primerclass [primerschemes]`: The primer class  [default: primerschemes]
-* `--collection [ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET]`: The collection
+* `--collection [ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP]`: The collection
 * `--link-protocol TEXT`: Optional link to protocol
 * `--link-validation TEXT`: Optional link to validation data
 * `--links-homepage TEXT`: Optional link to homepage
 * `--link-vendor TEXT`: Optional link to vendors
 * `--link-misc TEXT`: Optional miscellaneous link
 * `--fix / --no-fix`: Attempt to fix the scheme  [default: no-fix]
+* `--contact-info TEXT`: Contact information
+* `--additional-files PATH`: Additional files to include in the ./work directory
 * `--help`: Show this message and exit.
 
+
 ## `primal-page download`
 
 Download schemes from the index.json
@@ -276,13 +275,13 @@ Add a Collection to the Collection list in the info.json file
 **Usage**:
 
 ```console
-$ primal-page modify add-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}
+$ primal-page modify add-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}
 ```
 
 **Arguments**:
 
 * `SCHEMEINFO`: The path to info.json  [required]
-* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}`: The Collection to add  [required]
+* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}`: The Collection to add  [required]
 
 **Options**:
 
@@ -485,13 +484,13 @@ Remove an Collection from the Collection list in the info.json file
 **Usage**:
 
 ```console
-$ primal-page modify remove-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}
+$ primal-page modify remove-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}
 ```
 
 **Arguments**:
 
 * `SCHEMEINFO`: The path to info.json  [required]
-* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}`: The Collection to remove  [required]
+* `COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET|VARVAMP}`: The Collection to remove  [required]
 
 **Options**:
 

diff --git a/docs/examples.md b/docs/examples.md
@@ -13,7 +13,31 @@ From primalscheme a file should be output called `{scheme-name}.primer.bed`. Thi
 
 ![primerbed](assets/primalscheme1bed.png)
 
+### Using `primal-page`
 
+![primerbed](assets/primal-page-create.png)
+
+`primal-page` provides lots of options for creating the metadata. However, most of these are optional.
+
+#### Required options
+| Option               | Description                                    |
+| -------------------- | ---------------------------------------------- |
+| `--schemename`       | The name of the scheme                         |
+| `--ampliconsize`     | The amplicon size                             |
+| `--schemeversion`    | The version of the scheme                      |
+| `--species`          | The `taxid` of the target species              |
+| `--authors`          | The authors of the scheme                      |
+| `--schemestatus`     | The status of the scheme                       |
+| `--primerbed`        | A .bed file containing the primers             |
+| `--reference`        | A .fasta file containing the reference genomes |
+| `--output`           | Where to create the files                      |
+| `--algorithmversion` | Which version was used (`primalscheme1`)       |
+
+The requirements of these settings are listed in the [cli](cli.md)
+
+```
+primal-page create --schemename example-scheme --ampliconsize 400 --schemeversion v1.0.0 --species 1 --authors 'John Smith'  --authors 'Jane Doe' --schemestatus draft --primerbed {path to file} --reference {path to file} --output {~/primerschemes/primerschemes} --algorithmversion primalscheme1
+```
 
 
 ## Manual editing of files

diff --git a/primal_page/main.py b/primal_page/main.py
@@ -109,14 +109,14 @@ def create(
     primerbed: Annotated[
         pathlib.Path,
         typer.Option(
-            help="Manually specify the primer bed file, default is *primer.bed",
+            help="The path to the primer.bed file",
             readable=True,
         ),
     ],
     reference: Annotated[
         pathlib.Path,
         typer.Option(
-            help="Manually specify the reference.fasta file, default is *.fasta",
+            help="The path to the reference.fasta file",
             readable=True,
         ),
     ],