--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manipulate.xml	Wed Apr 10 03:25:05 2019 -0400
@@ -0,0 +1,217 @@
+<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>