# HG changeset patch
# User boris
# Date 1372135287 14400
# Node ID c340422b78b123f45a75fce4ab67e57a5cc0f1b9
# Parent  0f66636a3f8811a261b571db5afbad86fd58d4c4
Edited xml tool description

diff -r 0f66636a3f88 -r c340422b78b1 phylorelatives.xml
--- a/phylorelatives.xml	Fri Jun 14 13:38:45 2013 -0400
+++ b/phylorelatives.xml	Tue Jun 25 00:41:27 2013 -0400
@@ -40,12 +40,12 @@
     </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="Useful to generate background tree"/>
+    <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 ${on_string}: newick"/>
+    <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick string"/>
     <data format="png" name="plot"  label="${tool.name} on ${on_string}: tree plot"/>
   </outputs>
   <tests>
@@ -60,8 +60,8 @@
     
 
 
-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.
+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.
 
 -----
 
@@ -71,7 +71,7 @@
 
 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 per minor allele sequence, the tree plot and newick string of the tree.
+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.
 
 -----
 
@@ -80,7 +80,7 @@
 **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 if more than one FASTA file is provided.
+Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation of individual FASTA files.
 
 -----
 
@@ -92,22 +92,29 @@
 
 See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
 
+*Newick*
+
+http://www.megasoftware.net/WebHelp/glossary/rh_newick_format.htm
+
 -----
 
 **Example**
 
-- For the following dataset::
-    >sample1_major
-    >sample1_minor
-    >sample2_major
-    >sample3_major
-    >sample4_major
+- For the multiple alignment composed of the following FASTA files::
+
+   >sample1_major
+   >sample1_minor
+   >sample2_major
+   >sample3_major
+   >sample4_major
   
 
-- running this tool with *b = 1000*  *m = yes* *root = RSRS*,  will return::
-    newick
-    relatives
-    plot
+- 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)
 
 -----