<tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>matrix and annotations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
@CMD@
      ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_imports@
adata = ad.read_h5ad('$input')
adata.write_csvs('.', sep="\t", skip_data = False)
    ]]></configfile>
</configfiles>
    <inputs>
        <param name="input" type="data" format="h5ad" label="Annotated data matrix to export" help="Create individual tabular files for matrix, obs, obsm, var and varm annotations"/>
    </inputs>
    <outputs>
        <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"/>
        <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"/>
        <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"/>
        <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"/>
        <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"/>
    </outputs>
    <tests>
        <test expect_num_outputs="5">
            <param name="input" value="krumsiek11.h5ad"/>
            <assert_stdout>
                <has_text_matching expression="adata.write_csvs"/>
            </assert_stdout>
            <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/>
            <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/>
            <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/>
            <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
            <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
This tool exports an AnnData dataset to a tabular files (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)

@HELP@
    ]]></help>
    <expand macro="citations"/>
</tool>