From my experience using biocontainers base container no need to set yes installation is done without any command prompt, otherwise as for apt install use the flag -y it works (maybe depend the version of conda...).
So to install several tools you can do something like that to variate Chanels

# add dependencies via conda
RUN conda install -c bioconda samtools && \
         conda install -c anaconda python && \
         conda install  r-base

If you have many dependencies you can list them in a yaml file e.g. dep.yml:

name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - tool1
  - tool2=versionX
  - tool3

and then in your Dockerfile you do:

# copy YML dependency file
COPY dep.yml /tmp/dep.yml

# Install dependencies listed in dep.yml  file
RUN conda env update -n base --file /tmp/dep.yml