--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_unpack_pathways.xml	Wed May 12 09:07:12 2021 +0000
@@ -0,0 +1,66 @@
+<tool id="humann_unpack_pathways" name="Unpack pathway abundances" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>to show the genes for each</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+humann_unpack_pathways
+    --input-genes '$input_genes'
+    --input-pathways '$input_pathways'
+#if $gene_mapping
+    --gene-mapping '$gene_mapping'
+#end if
+#if $pathway_mapping
+    --pathway-mapping '$pathway_mapping'
+#end if
+    $remove_taxonomy
+    --output '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--input-genes" type="data" format="tsv,tabular" label="Gene family or EC abundance file"/>
+        <param argument="--input-pathways" type="data" format="tsv,tabular" label="Pathway abundance file"/>
+        <param argument="--gene-mapping" type="data" format="tsv,tabular" optional="true" label="Gene family to reaction mapping file"/>
+        <param argument="--pathway-mapping" type="data" format="tsv,tabular" optional="true" label="Reaction to pathway mapping file"/>
+        <param argument="--remove-taxonomy" type="boolean" truevalue="--remove-taxonomy" falsevalue="" checked="false" label="Remove the taxonomy from the output file?"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_genes" value="demo_genefamilies.tsv"/>
+            <param name="input_pathways" value="demo_pathabundance.tsv"/>
+            <param name="remove_taxonomy" value=""/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text="humann_Abundance"/>
+                    <has_text text="PWY-4203|unclassified|UniRef90_Q6XMI3"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_genes" value="demo_genefamilies.tsv"/>
+            <param name="input_pathways" value="demo_pathabundance.tsv"/>
+            <param name="remove_taxonomy" value="--remove-taxonomy"/>
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_text text="humann_Abundance"/>
+                    <has_text text="PWY-4203|UniRef90_Q6XMI3"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This tool unpacks the pathways to show the genes for each.
+
+It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>