<tool id="drug2cell" name="drug2cell" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>Collection of utility functions for gene group activity evaluation in scanpy</description>
     <macros>
        <token name="@TOOL_VERSION@">0.1.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="0.1.2">drug2cell</requirement>
        <requirement type="package" version="1.10.4">scanpy</requirement>
    </requirements>

 <command>
    <![CDATA[
    python3 '$script' --adata '${adata}' --output '${d2c_output}'
    ]]>
 </command>
 <configfiles>
    <configfile name="script">
<![CDATA[
import drug2cell as d2c
import scanpy as sc
        
# Load AnnData object
adata = sc.read_h5ad("${adata}")

# Run drug2cell
d2c.score(adata)

# Get the drug2cell results
d2cell = adata.uns["drug2cell"]

# Save the drug2cell results to a new .h5ad file
d2cell.write("${d2c_output}")
]]>
    </configfile>
 </configfiles>

 <inputs>
     <param name="adata" type="data" format="h5ad" label="AnnData Object" help="Select the processed AnnData object file containing your single-cell RNA-seq data"/>
 </inputs>

 <outputs>
    <data name="d2c_output" format="h5ad" label="drug2cell Results" />
 </outputs>

<tests>
    <test>
        <param name="adata" value="tiny_adata.h5ad"/>
        <output name="d2c_output" file="d2c_output.h5ad">
            <assert_contents>
                <has_h5_keys keys="obs,var"/>
            </assert_contents>
        </output>
    </test>
</tests>

<help>
    <![CDATA[
    This tool uses the drug2cell package to score gene groups based on drug-target data from the ChEMBL database.
    It performs differential expression analysis to identify gene groups up-regulated in particular clusters.
    ]]>
</help>


<citations>
    <citation type="doi">10.1038/s41586-023-06311-1</citation>
 </citations>
</tool>