<tool id="scimap_anndata_to_csv" name="Convert Anndata to CSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>with Scimap</description>
    <macros>
        <import>main_macros.xml</import>
    </macros>
    <expand macro="scimap_requirements" />
    <expand macro="macro_stdio" />
    <version_command>echo "@VERSION@"</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
        python '$__tool_directory__/anndata_to_csv.py'
            --inputs '$inputs'
            --outfile '$outfile'

        ]]>
    </command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
        <param name="layer" type="select" label="Select the Anndata layer to export">
            <option value="x">adata.X</option>
            <option value="raw">adata.raw.X</option>
        </param>
        <param name="cellid" type="text" value="CellID" label="Name of column containing Cell IDs" />
    </inputs>
    <outputs>
        <data format="csv" name="outfile" />
    </outputs>
    <tests>
        <test>
            <param name="anndata" value="tutorial_data.h5ad" />
            <param name="layer" value="x" />
            <output name="outfile" ftype="csv">
                <assert_contents>
                    <has_n_columns n="41" sep="," />
                    <has_n_lines n="500" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

This scimap function converts from Anndata format to CSV.
There are three options for the data matrix returned: 
1) the current contents of adata.X
2) the current contents of adata.raw.X
3) the current contents of adata.raw.X with a log+1 transformation applied 

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