<tool id="anndata_manipulate" name="Manipulate AnnData" version="@VERSION@+@GALAXY_VERSION@">
    <description>object</description>
    <macros>
        <import>macros.xml</import>
        <xml name="param_join">
            <param name="join" type="select" label="The connecting string between name and integer">
                <option value="-">-</option>
                <option value="_">_</option>
                <option value=" "> </option>
                <option value="/">/</option>
            </param>
        </xml>
    </macros>
    <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('$input')

#if $manipulate.function == 'concatenate'
    #for i, filepath in enumerate($manipulate.other_adatas)
adata_$i = ad.read('$filepath')
    #end for
adata.concatenate(
    #for i, filepath in enumerate($manipulate.other_adatas)
    adata_$i,
    #end for
    join='$manipulate.join',
    #if str($manipulate.index_unique) != ''
    index_unique='$manipulate.index_unique',
    #else
    index_unique=None,
    #end if
    batch_key='$manipulate.batch_key')

#else if $manipulate.function == 'var_names_make_unique'
adata.var_names_make_unique(join='$manipulate.join')

#else if $manipulate.function == 'obs_names_make_unique'
adata.obs_names_make_unique(join='$manipulate.join')

#else if $manipulate.function == 'rename_categories'
    #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
adata.rename_categories(
    key='$manipulate.key',
    categories=$categories)

#else if $manipulate.function == 'transpose'
adata.transpose()

#else if $manipulate.function == 'strings_to_categoricals'
adata.strings_to_categoricals()
#end if

adata.write('anndata.h5ad')
]]></configfile>
    </configfiles>
    <inputs>
        <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
        <conditional name="manipulate">
            <param name="function" type="select" label="Function of manipulate the object">
                <option value="concatenate">Concatenate along the observations axis</option>
                <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
                <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
                <option value="rename_categories">Rename categories of annotation</option>
                <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
                <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
            </param>
            <when value="concatenate">
                <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
                <param name="join" type="select" label="Join method">
                    <option value="inner">Intersection of variables</option>
                    <option value="outer">Union of variables</option>
                </param>
                <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
                <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">
                    <option value="-">-</option>
                    <option value="_">_</option>
                    <option value=" "> </option>
                    <option value="/">/</option>
                </param>
            </when>
            <when value="obs_names_make_unique">
                <expand macro="param_join"/>
            </when>
            <when value="var_names_make_unique">
                <expand macro="param_join"/>
            </when>
            <when value="rename_categories">
                <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
                <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
            </when>
            <when value="strings_to_categoricals"/>
            <when value="transpose"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="concatenate"/>
                <param name="other_adatas" value="import.csv.h5ad"/>
                <param name="join" value="inner"/>
                <param name="batch_key" value="batch"/>
                <param name="index_unique" value="-"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata_0"/>
                <has_text_matching expression="adata.concatenate"/>
                <has_text_matching expression="join='inner'"/>
                <has_text_matching expression="index_unique='-'"/>
                <has_text_matching expression="batch_key='batch'"/>
            </assert_stdout>
            <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="obs_names_make_unique"/>
                <param name="join" value="-"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
            </assert_stdout>
            <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="var_names_make_unique"/>
                <param name="join" value="-"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
            </assert_stdout>
            <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="rename_categories"/>
                <param name="key" value="cell_type"/>
                <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.rename_categories"/>
                <has_text_matching expression="key='cell_type'"/>
                <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
            </assert_stdout>
            <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="strings_to_categoricals"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.strings_to_categoricals"/>
            </assert_stdout>
            <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test>
            <param name="input" value="krumsiek11.h5ad"/>
            <conditional name="manipulate">
                <param name="function" value="transpose"/>
            </conditional>
            <assert_stdout>
                <has_text_matching expression="adata.transpose"/>
            </assert_stdout>
            <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool takes a AnnData dataset, manipulates it and returns it. 

The possible manipulations are: 

- Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__) 

    The `uns`, `varm` and `obsm` attributes are ignored.

    If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN`

- Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__) 

    The first occurance of a non-unique value is ignored.

- Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__) 

    The first occurance of a non-unique value is ignored.

- Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__) 

    Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`

- Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__) 

    Only affects string annotations that lead to less categories than the total number of observations.

- Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__)

    Data matrix is transposed, observations and variables are interchanged.

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