--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_abundance_taxonomy.xml	Mon Sep 14 08:07:43 2020 +0000
@@ -0,0 +1,86 @@
+<tool id="phyloseq_taxonomy" name="Phyloseq Abundance Taxonomy" version="1.22.3.3" hidden="false">
+  <description>Phyloseq Abundance Plot on Taxonomy level</description>
+  <requirements>
+      <requirement type="package" version="3.4.1">r-base</requirement>
+      <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
+      <requirement type="package" version="1.20.0">r-getopt</requirement>
+      <requirement type="package" version="9.18">ghostscript</requirement>
+  </requirements>
+  <version_command><![CDATA[
+	  echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+ ]]></version_command>
+  <command detect_errors="exit_code"><![CDATA[
+   Rscript '${__tool_directory__}/phyloseq_abundance_taxonomy.r' 
+   		--biomfile='$biom_input' 
+		--metafile='$metadata_input' 
+		--xcolumn="${xaxis_column}" 
+		--lcolumn="${legend_column}" 
+		--taxonomy="${taxonomy_rank}" 
+		--outdir="$htmlfile.files_path" 
+		--htmlfile='$htmlfile'
+  ]]></command>
+ 
+  <inputs>
+    <param format="biom1" name="biom_input" type="data" label="BIOM file"/>
+    <param format="tabular" name="metadata_input" type="data" label="Metadata file"/>
+    <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/>
+    <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/>
+    <param name="taxonomy_rank" type="select" display="radio" label="Select a taxonomy rank">
+      <option value="Kingdom" selected="true">Kingdom</option>
+      <option value="Phylum">Phylum</option>
+      <option value="Class">Class</option>
+      <option value="Order">Order</option>
+      <option value="Family">Family</option>
+      <option value="Genus">Genus</option>
+      <option value="Species">Species</option>
+    </param>
+  </inputs>
+ 
+  <outputs>
+        <data format="html" name="htmlfile" label="${tool.name}.html"/>
+  </outputs>
+  
+  <tests>
+  	<test>
+		<param name="biom_input" value="test.biom" ftype="biom1" />
+		<param name="metadata_input" value="metadata.txt" />
+		<param name="xaxis_column" value="5" />
+		<param name="legend_column" value="4" />
+		<param name="taxonomy_rank" value="Phylum" />
+		<output name="htmlfile" ftype="html" file="biom_out.html" />
+	</test>
+  </tests>
+  <help>
+**What it does**
+Creates an abundance with taxonomy barplot using an R package called phyloseq_.
+
+.. _phyloseq: https://joey711.github.io/phyloseq/plot_bar-examples.html
+
+-----
+
+**Input**
+
+
+- **BIOM file** - this is a BIOM_ file format
+- **Metadata file** - this is a metadata file of the experiment design
+- **Column used for X-axis** - The horizontal x-axis display on the barplot.
+- **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to.
+- **Select a taxonomy rank** - This is a taxonomy selection.
+
+
+.. _BIOM: http://biom-format.org/
+
+-----
+
+=========
+Resources
+=========
+
+**Wrapper Authors**
+QFAB Bioinformatics (support@qfab.org)
+
+  </help>
+  <citations>
+	   <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
+  </citations>
+</tool>