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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata2ri/ commit f2b398613762cdee5f89fb43382df2bf7321ccde

<tool id="anndata2ri" name="anndata2ri" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
    <description>
        Convert between Anndata and SingCellExperiment objects
    </description>
    <macros>
        <token name="@TOOL_VERSION@">1.3.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">anndata2ri</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">anndata2ri</requirement>
        <requirement type="package" version="0.10.9">anndata</requirement>
        <requirement type="package" version="1.24.0">bioconductor-singlecellexperiment</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
            python '$script_file' '$conversion.direction'
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
import sys
import anndata as ad
import anndata2ri
import rpy2.robjects as ro
from rpy2.rlike.container import OrdDict

ro.r('suppressPackageStartupMessages(library(SingleCellExperiment))')

def convert_orddict_to_dict(uns):
    if isinstance(uns, OrdDict):
        return {k: convert_orddict_to_dict(v) for k, v in uns.items()}
    elif isinstance(uns, list):
        return [convert_orddict_to_dict(v) for v in uns]
    elif isinstance(uns, tuple):
        return tuple(convert_orddict_to_dict(v) for v in uns)
    elif isinstance(uns, dict):
        return {k: convert_orddict_to_dict(v) for k, v in uns.items()}
    else:
        return uns

if sys.argv[1] == 'sce2anndata':
    sce = ro.r('readRDS')('$conversion.input_object')
    with ro.conversion.localconverter(ro.default_converter + anndata2ri.converter):
        adata = ro.conversion.rpy2py(sce)
    adata.uns = convert_orddict_to_dict(adata.uns)
    adata.obs.index = adata.obs.index.astype(str)
    adata.var.index = adata.var.index.astype(str)
    adata.write('outfile.h5ad', compression='gzip')

elif sys.argv[1] == 'anndata2sce':
    adata = ad.read_h5ad('$conversion.input_object')
    with ro.conversion.localconverter(ro.default_converter + anndata2ri.converter):
        sce = ro.conversion.py2rpy(adata)
    ro.r('saveRDS')(sce, 'outfile.rds')

        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="conversion" >
            <param name="direction" type="select" label="Convert From / To" >
                <option value="sce2anndata" >SingleCellexperiment to AnnData</option>
                <option value="anndata2sce" >AnnData to SingleCellexperiment</option>
            </param>
            <when value="sce2anndata">
                <param name="input_object" type="data" format="rdata.sce,rds" label="SingCellExperiment object to convert" />
            </when>
            <when value="anndata2sce" >
                <param name="input_object" type="data" format="h5ad,h5" label="Anndata object to convert"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_anndata" format="h5ad" from_work_dir="outfile.h5ad" label="${tool.name} on ${on_string}: Anndata object">
            <filter>conversion['direction'] == 'sce2anndata'</filter>
        </data>
        <data name="output_sce" format="rdata.sce" from_work_dir="outfile.rds" label="${tool.name} on ${on_string}: SingleCellExperiment object">
            <filter>conversion['direction'] == 'anndata2sce'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="direction" value="sce2anndata"/>
            <param name="input_object" value="krumsiek11.rds"/>
            <output name="output_anndata" file="krumsiek11.h5ad" ftype="h5ad" compare="sim_size">
                <assert_contents>
                    <has_h5_keys keys="obs/cell_type"/>
                    <has_h5_keys keys="uns/highlights"/>
                    <has_h5_keys keys="uns/iroot"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="direction" value="anndata2sce"/>
            <param name="input_object" value="krumsiek11.h5ad"/>
            <output name="output_sce" file="krumsiek11.rds" ftype="rdata.sce" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
anndata2ri
==========
        Convert between Anndata and SingleCellExperiment objects. For conversion of further single-cell file formats, consider using **SCEasy Converter** tool.
    ]]></help>
    <citations>
        <citation type="bibtex">
        @unpublished{anndata2ri,
            author = {Theis Lab},
            title = {Convert between AnnData and SingleCellExperiment },
            url = {https://github.com/theislab/anndata2ri}
        }
        </citation>
    </citations>
</tool>