diff humann_genefamilies_genus_level @ 0:ec422794133f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/humann_genefamilies_genus_level	Wed May 12 09:01:24 2021 +0000
@@ -0,0 +1,52 @@
+<!-- The tool is broken with current version of HUMAnN. Once it will be fixed (PR merged), we can update this wrapper and add the XML extension to enable it -->
+<tool id="humann_genefamilies_genus_level" name="Create a genus level" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>gene families and pathways from HUMAnN species level 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_genefamilies_genus_level 
+    --input '$input'
+    --output '$gene_families'
+&&
+humann
+    --input '$gene_families'
+    --output '$pathways'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tsv,tabular" label="Species level gene families" help="Direct output from HUMAnN"/>
+    </inputs>
+    <outputs>
+        <data name="gene_families" format="tabular" label="${tool.name} on ${on_string}: Genus level gene families"/>
+        <data name="pathways" format="tabular" label="${tool.name} on ${on_string}: Genus level pathways"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="demo_genefamilies.tsv"/>
+            <output name="gene_families" ftype="tabular" value="genus-level-gene-families.tsv" compare="sim_size">
+                <assert_contents>
+                    <has_text text="humann_Abundance"/>
+                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output name="pathways" ftype="tabular" value="genus-level-pathways.tsv" compare="sim_size">
+                <assert_contents>
+                    <has_text text="humann_Abundance"/>
+                    <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+By default, the gene families and pathways output files from HUMAnN are species level.
+This tool generates genus level gene families and pathways
+    ]]></help>
+    <expand macro="citations"/>
+</tool>