<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>