--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify_loom.xml	Mon Jan 06 13:43:38 2020 -0500
@@ -0,0 +1,72 @@
+<tool id="modify_loom" name="Manipulate loom object" version="@VERSION@+@GALAXY_VERSION@">
+    <description>Add layers, or row/column attributes to a loom file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/modify_loom.py' -f '${input}'
+#if $which_add.add_type == "cols":
+    -a cols -c '${which_add.cols}'
+#else if $which_add.add_type == "cols":
+    -a rows -r '${which_add.rows}'
+#else if $which_add.add_type == "layers":
+    -a layers -l '${which_add.layers}'
+#end if
+&& cp '${input}' loom_add_out.loom
+      ]]></command>
+    <inputs>
+        <param name="input" type="data" format="loom" label="Loom file"/>
+        <conditional name="which_add">
+            <param name="add_type" type="select" label="Select data attribute to add to loom">
+                <option value="cols">Columns</option>
+                <option value="rows">Rows</option>
+                <option value="layers">Layers</option>
+            </param>
+            <when value="cols">
+                <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
+            </when>
+            <when value="rows">
+                <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
+            </when>
+            <when value="layers">
+                <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="loomout" format="loom" from_work_dir='loom_add_out.loom' label="Expanded loom file from '${on_string}'"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="addtest.loom"/>
+            <param name="add_type" value="cols"/>
+            <param name="cols" value="cols.tsv"/>
+            <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="addtest.loom"/>
+            <param name="add_type" value="rows"/>
+            <param name="rows" value="rows.tsv"/>
+            <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="addtest.loom"/>
+            <param name="add_type" value="layers"/>
+            <param name="layers" value="addlayer1.tsv"/>
+            <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
+            author = "Linnarsson lab"
+            title = "Loompy"
+            year = "2013"
+            note = "https://github.com/linnarsson-lab/loompy"}
+        </citation>
+    </citations>
+</tool>