--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_infer_taxonomy	Mon Feb 13 16:16:49 2023 +0000
@@ -0,0 +1,81 @@
+<!-- The tool is broken with current version of HUMAnN. Once it will be fixed, we can update this wrapper and add the XML extension to enable it -->
+<tool id="humann_infer_taxonomy" name="Infex taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>for "unclassified" taxonomy in HUMAnN generated gene families</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+humann_infer_taxonomy
+    --input '$input'
+    --output '$output'
+    --level '$level'
+    --database '$database.fields.path'
+    --mode '$mode'
+    --lca-choice '$lca_choice'
+    --threshold $threshold
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular" label="Gene family table"/>
+        <param argument="--level" type="select" label="Desired level for taxonomic estimation/summation">
+            <option value="Kingdom">Kingdom</option>
+            <option value="Phylum">Phylum</option>
+            <option value="Class">Class</option>
+            <option value="Order">Order</option>
+            <option value="Family" selected="true">Family</option>
+            <option value="Genus">Genus</option>
+        </param>
+        <param argument="--database" type="select" label="UniRef-specific taxonomy database">
+            <options from_data_table="humann_utility_mapping">
+                <validator message="No utility mapping is available" type="no_options" />
+                <filter type="regexp" column="2" value="tol-lca" />
+            </options>
+        </param>
+        <param argument="--mode" type="select" label="Rows to include in the estimation/summation">
+            <option value="c_tmode" selected="true">Totals</option>
+            <option value="c_umode">Unclassified</option>
+            <option value="c_smode">Stratified</option>
+        </param>
+        <param argument="--lca-choice" type="select" label="Per-gene taxonomic annotation to consider">
+            <option value="source_tax">Source taxonomy</option>
+            <option value="uniref_lca">UniRef lowest common ancestor (LCA)</option>
+            <option value="humann_lca" selected="true">HUMAnN lowest common ancestor (LCA)</option>
+        </param>
+        <param argument="--threshold" type="float" value="1e-3" label="Minimum frequency for a new taxon to be included"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value=""/>
+            <param name="level" value="Kingdom"/>
+            <param name="database" value=""/>
+            <param name="mode" value="c_tmode"/>
+            <param name="lca_choice" value="source_tax"/>
+            <param name="threshold" value="1e-3"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text=""/>
+                    <has_line line=""/>
+                    <has_line_matching expression=""/>
+                    <has_n_columns n=""/>
+                    <has_size value="" delta=""/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Based on the lowest common ancestor (LCA) annotation
+of each UniRef50/90 cluster, this tool infers approximate taxonomy 
+for unclassified features at a target level of resolution.
+
+It will modify features of known genus/species to match 
+target level.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>