Viash Hub

Description

Scale data to unit variance and zero mean.

Arguments

Name	Type & Properties	Description
--input -i	file required	Input h5mu file.
--modality	string	List of modalities to process.
--input_layer	string	Input layer with data to scale. Uses .X by default
--output_layer	string	Output layer where scaled data will be stored. If not specified, .X will be used.
--max_value	double	Clip (truncate) to this value after scaling. Does not clip by default.
--zero_center	boolean_false	If set, omit zero-centering variables, which allows to handle sparse input efficiently.
--output -o	file required output	Output h5mu file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--output_layer

string

--max_value

double

--zero_center

boolean_false

--output

-o

file

required

output

--output_compression

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/transform/scale/main.nf \  
  -params-file params.yaml

Relationships

Used by

1 relationships

workflows/rna/rna_multisampleopenpipeline v4.0.0

Current component

transform/scaleopenpipeline v4.0.0

Uses

0 relationships

No component dependencies found.