--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export.xml	Wed Apr 10 03:24:14 2019 -0400
@@ -0,0 +1,82 @@
+<tool id="anndata_export" name="Export AnnData" version="@VERSION@+@GALAXY_VERSION@">
+    <description>to different formats</description>
+    <macros>
+        <import>macros.xml</import>
+    </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 $output_format == 'loom'
+adata.write_loom('anndata.loom')
+#else if $output_format == 'tabular'
+adata.write_csvs('.', sep="\t", skip_data = False)
+#end if
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
+        <param name="output_format" type="select" label="Format to write the annotated data matrix">
+            <option value="loom">loom</option>
+            <option value="tabular">Tabular</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix">
+            <filter>output_format == 'loom'</filter>
+        </data>
+        <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)">
+            <filter>output_format == 'tabular'</filter>
+        </data>
+        <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
+            <filter>output_format == 'tabular'</filter>
+        </data>
+        <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
+            <filter>output_format == 'tabular'</filter>
+        </data>
+        <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
+            <filter>output_format == 'tabular'</filter>
+        </data>
+        <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
+            <filter>output_format == 'tabular'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <param name="output_format" value="loom"/>
+            <assert_stdout>
+                <has_text_matching expression="adata.write_loom"/>
+            </assert_stdout>
+            <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input" value="krumsiek11.h5ad"/>
+            <param name="output_format" value="tabular"/>
+            <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[
+**What it does**
+
+This tool exports a AnnData dataset to a Loom file 
+(`write_loom method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_loom.html>`__) 
+or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.write_csvs.html>`__)
+
+@HELP@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>