--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylorelatives.xml	Mon Feb 03 13:01:44 2014 -0500
@@ -0,0 +1,125 @@
+<tool id="phylorelatives" name="Phylorelatives" version="0.0.1">
+  <description>Relatedness of minor alelle sequences in NJ tree</description>
+  <requirements>
+    <requirement type="package" version="2.15.0">R</requirement>
+    <requirement type="package" version="2.2.6">rpy2</requirement>
+    <requirement type="package" version="3.12.0">dendropy</requirement>
+    <requirement type="package" version="3.0-8">ape</requirement>
+  </requirements>
+  <command interpreter="python">phylorelatives.py
+     #for $sequence in ( $sequences ):
+         -i "${sequence}"
+     #end for
+     -m "${multifasta}"
+     -b "$iterations"
+     $pairwise
+     $major_only
+     #if str($root.root_selector)=="add_root":
+      -r "${root.root_fa}"
+     #end if
+     --relatives-out "$siblings"
+     --newick-out "$newick"
+     --trees-out "$plot"
+  </command>
+  <inputs>
+      <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
+      </param>
+    <conditional name="root">
+      <param name="root_selector" type="select" label=" Root sequence">
+        <option value="unrooted" selected="True"></option>
+        <option value="add_root"></option>
+      </param>
+      <when value="unrooted">
+      </when>           
+      <when value="add_root">
+        <param name="root_fa" format="fasta" type="data"  label="Root tree using" help="Must have the same length as input sequences"/>
+      </when>
+    </conditional>
+    <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to &quot;Complete deletion&quot;"/>
+    <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>
+    <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="All sequences will be treated as major allele sequences. Useful to generate background tree"/>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta used" />
+    <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives list"/>
+    <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick string"/>
+    <data format="png" name="plot"  label="${tool.name} on ${on_string}: tree plot"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="iterations" value="0"/>
+      <param name="sequences" value="test.fa"/>
+      <output name="siblings" file="test.fa-siblings.tab"/>
+    </test>
+  </tests>
+
+  <help>
+    
+
+
+The major and minor allele sequences of a sample are expected to cluster together in a phylogenetic tree.
+Deviation from expectation suggests potential contamination coming from the closest unrelated samples.
+
+-----
+
+.. class:: infomark
+
+**What it does**
+
+Constructs relatedness of a set of sequences based on the pairwise proportion of different sites.
+One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor).
+It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives, the tree plot and newick string of the tree.
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+This tools DOES NOT align the sequences.
+Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation of individual FASTA files.
+
+-----
+
+.. class:: infomark
+
+**About formats**
+
+*FASTA multiple alignment*
+
+See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
+
+*Newick*
+
+http://www.megasoftware.net/WebHelp/glossary/rh_newick_format.htm
+
+-----
+
+**Example**
+
+- For the multiple alignment composed of the following FASTA files::
+
+   >sample1_major
+   >sample1_minor
+   >sample2_major
+   >sample3_major
+   >sample4_major
+  
+
+- running this tool with *root = RSRS.fasta*, and default parameters will return four datasets::
+ 
+   1. multiple alignment file used for running the tool
+   2. relatives of sample1_minor
+   3. NJ tree newick string (rooted on RSRS)
+   4. NJ tree png plot (rooted on RSRS)
+
+-----
+
+**Citation**
+
+If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.*
+(boris-at-bx.psu.edu)
+
+  </help>
+
+</tool>
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