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document arguments with multiple true
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@rcannood
rcannood committed Sep 8, 2023
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6 changes: 3 additions & 3 deletions components/modules/annotate/popv.qmd
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Expand Up @@ -127,9 +127,9 @@ Output arguments.
Other arguments.


|Name |Description |Attributes |
|:-----------|:-----------------------------------------------------------------------|:-----------------------------------------------------------------|
|`--methods` |Methods to call cell types. By default, runs to knn_on_scvi and scanvi. |`string`, required, example: `"knn_on_scvi"`, example: `"scanvi"` |
|Name |Description |Attributes |
|:-----------|:-----------------------------------------------------------------------|:-----------------------------------------------------------------------------------|
|`--methods` |Methods to call cell types. By default, runs to knn_on_scvi and scanvi. |List of `string`, required, example: `"knn_on_scvi", "scanvi"`, multiple_sep: `":"` |

## Authors

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18 changes: 9 additions & 9 deletions components/modules/cluster/leiden.qmd
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Expand Up @@ -80,15 +80,15 @@ Replace `-profile docker` with `-profile podman` or `-profile singularity` depen

### Arguments

|Name |Description |Attributes |
|:-----------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------------------------------------|
|`--input` |Input file. |`file`, required, example: `"input.h5mu"` |
|`--modality` | |`string`, default: `"rna"` |
|`--obsp_connectivities` |In which .obsp slot the neighbor connectivities can be found. |`string`, default: `"connectivities"` |
|`--output` |Output file. |`file`, required, example: `"output.h5mu"` |
|`--output_compression` | |`string`, example: `"gzip"` |
|`--obsm_name` |Name of the .obsm key under which to add the cluster labels. The name of the columns in the matrix will correspond to the resolutions. |`string`, default: `"leiden"` |
|`--resolution` |A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters. Multiple values will result in clustering being performed multiple times. |`double`, default: `1` |
|Name |Description |Attributes |
|:-----------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------|
|`--input` |Input file. |`file`, required, example: `"input.h5mu"` |
|`--modality` | |`string`, default: `"rna"` |
|`--obsp_connectivities` |In which .obsp slot the neighbor connectivities can be found. |`string`, default: `"connectivities"` |
|`--output` |Output file. |`file`, required, example: `"output.h5mu"` |
|`--output_compression` | |`string`, example: `"gzip"` |
|`--obsm_name` |Name of the .obsm key under which to add the cluster labels. The name of the columns in the matrix will correspond to the resolutions. |`string`, default: `"leiden"` |
|`--resolution` |A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters. Multiple values will result in clustering being performed multiple times. |List of `double`, default: `1`, multiple_sep: `":"` |

## Authors

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12 changes: 6 additions & 6 deletions components/modules/convert/from_h5ad_to_h5mu.qmd
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Expand Up @@ -68,12 +68,12 @@ Replace `-profile docker` with `-profile podman` or `-profile singularity` depen

### Arguments

|Name |Description |Attributes |
|:----------------------|:-------------------|:-----------------------------------------|
|`--input` |Input h5ad files |`file`, required, default: `"input.h5ad"` |
|`--modality` | |`string`, default: `"rna"` |
|`--output` |Output MuData file. |`file`, default: `"output.h5mu"` |
|`--output_compression` | |`string`, example: `"gzip"` |
|Name |Description |Attributes |
|:----------------------|:-------------------|:----------------------------------------------------------------------|
|`--input` |Input h5ad files |List of `file`, required, default: `"input.h5ad"`, multiple_sep: `":"` |
|`--modality` | |List of `string`, default: `"rna"`, multiple_sep: `":"` |
|`--output` |Output MuData file. |`file`, default: `"output.h5mu"` |
|`--output_compression` | |`string`, example: `"gzip"` |

## Authors

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