# HG changeset patch
# User boris
# Date 1371230869 14400
# Node ID 6935429eef053673d2aa51e427b136ca50e0a4cb
# Parent  8d663949bdc89e3283ee288263f579024b62d2c0
Updfated xml with -j option

diff -r 8d663949bdc8 -r 6935429eef05 phylorelatives.xml
--- a/phylorelatives.xml	Mon Jun 10 00:48:11 2013 -0400
+++ b/phylorelatives.xml	Fri Jun 14 13:27:49 2013 -0400
@@ -13,6 +13,7 @@
      -m "${multifasta}"
      -b "$iterations"
      $pairwise
+     $major_only
      #if str($root.root_selector)=="upload_root":
       -r "${root.root_fa}"
      #end if
@@ -23,7 +24,7 @@
   </command>
   <inputs>
     <repeat name="sequences" title="Input FASTA file" min="1" help="Files will be concatenated into a single FASTA multiple alignment file, thus equal length homologous sequences are required">
-      <param format="fasta" name="sequence" type="data" label="FASTA file" help="Requires at least one minor allele sequence properly labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
+      <param format="fasta" name="sequence" type="data" label="FASTA file" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
       </param>
     </repeat>
     <conditional name="root">
@@ -38,11 +39,12 @@
       </when>
     </conditional>
     <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to &quot;Complete deletion&quot;"/>
-    <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>  
+    <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/>
+    <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="Useful to generate background tree"/>
   </inputs>
   <outputs>
-    <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" />
-    <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/>
+    <data format="fasta" name="multifasta" label="${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 ${on_string}: newick"/>
     <data format="txt" name="plot"  label="${tool.name} on ${on_string}: ascii plot"/>
   </outputs>
@@ -58,6 +60,9 @@
     
 
 
+Major allele and its closely related minor allele sequence are expected to cluster together in a tree.
+Deviation from expectation allows to trace back potential contamination from unrelated samples.
+
 -----
 
 .. class:: infomark