--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phyloseq_2_deseq2.xml	Mon Sep 14 08:20:41 2020 +0000
@@ -0,0 +1,90 @@
+<tool id="phyloseq_DESeq2" name="DESeq2" version="1.22.3" hidden="false">
+  <description>Differential Analysis</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>