<tool id="phyloseq_DESeq2" name="Phyloseq DESeq2" version="1.22.3" hidden="false">
  <description>Perform differential expression analysis of BIOM file</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="1.18.1">bioconductor-deseq2</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_2_deseq2.r' 
		--biomfile='$biom_input'
		--metafile='$metadata_input' 
		--factor="${factor}" 
		--test="${test}" 
		--fitType="${fitType}" 
		--cutoff='${cutoff}'
		--result='$DE_table'
		--normalisedResult='$normalised_table'
  ]]></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="factor" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="factor for differential analysis testing"/>
    <param name="test" type="select" display="radio" label="select a test statistic">
      <option value="Wald" selected="true">Wald</option>
      <option value="LRT">LRT</option>
    </param>
    <param name="fitType" type="select" display="radio" label="select a fit Type for dispersions">
      <option value="parametric" selected="true">parametric</option>
      <option value="local">local</option>
    </param>
    <param name="cutoff" value="0.05" type="float" label="cutoff value for differential analysis"/>
  </inputs>
 
  <outputs>
        <data format="tabular" name="DE_table" label="${tool.name} DE.txt"/>
        <data format="tabular" name="normalised_table" type="float" label="${tool.name} Normalised Table.txt"/>
  </outputs>

 <tests>
 	<test>  <!-- Test : Test BIOM format input -->
		<param name="biom_input" value="test.biom" ftype="biom1" />
		<param name="metadata_input" value="metadata.txt"/>
		<param name="factor" value="3" />
		<param name="test" value="Wald" />
		<param name="fitType" value="parametric" />
		<param name="cutoff" value="0.05"/>
		<output name="DE_table" ftype="tabular" file="DE_table.txt" />
		<output name="norm_DE_table" ftype="tabular" file="norm_DE_table.txt" />
	</test>
 </tests>
  <help>
**What it does**
Use BIOM and metadata file as input to perform a differential analysis using R package, DESeq2_ and Phyloseq_.

.. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
.. _Phyloseq: https://joey711.github.io/phyloseq/index.html

-----

**Input**

- **BIOM file** - select BIOM file
- **Metadata file** - metadata file contains experimental information.
- **factor for differential analysis testing** - select a factor for differential analysis testing
- **Select a test statistic** - e.g. Wald or LRT
- **Select a fit Type for dispersions** - e.g. parametric or local
- **cutoff value for differential analysis** - e.g. 0.05

-----


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

**Wrapper Authors**

QFAB Bioinformatics (support@qfab.org)
  </help>
  <citations>
      <citation type="doi">10.18129/B9.bioc.phyloseq</citation>
      <citation type="doi">10.1186/s13059-014-0550-8</citation>
  </citations>
</tool>