<tool id="phyloseq_richness" name="Phyloseq Richness" version="1.22.3.2" hidden="false">
  <description>Phyloseq Richness Plot</description>
     <requirements>
	         <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_richness.r' 
			--biomfile='$biom_input' 
			--metafile='$metadata_input' 
			--xcolumn="${xaxis_column}" 
			--lcolumn="${legend_column}" 
			--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"/>
  </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" />
		<output name="htmlfile" ftype="html" file="biom_out.html" />
	</test>
 </tests>


  <help>
**What it does**
Creates an alpha biodivesrsity abundance plot using an R package called phyloseq_.

.. _phyloseq: https://joey711.github.io/phyloseq/plot_richness-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.

.. _BIOM: http://biom-format.org/

-----

=========
Resources
=========

**Wrapper Authors**

QFAB Bioinformatics (support@qfab.org)
 
  </help>
    <citations>
	    <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
		<citation type="doi">doi:10.1186/2047-217X-1-7</citation>
	</citations>
 -----
 
  </help>
</tool>