# HG changeset patch
# User boris
# Date 1370839429 14400
# Node ID 034181b4b1b8697f985ff7933945c36d93329ee3
# Parent  75dcc9910f6d3f6738b2560e37a3be3943436154
Uploaded

diff -r 75dcc9910f6d -r 034181b4b1b8 phylorelatives.xml
--- a/phylorelatives.xml	Mon Jun 10 00:43:11 2013 -0400
+++ b/phylorelatives.xml	Mon Jun 10 00:43:49 2013 -0400
@@ -44,7 +44,7 @@
     <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" />
     <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/>
     <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick"/>
-    <data format="png" name="plot"  label="${tool.name} on ${on_string}: plot"/>
+    <data format="txt" name="plot"  label="${tool.name} on ${on_string}: ascii plot"/>
   </outputs>
   <tests>
     <test>
@@ -58,10 +58,6 @@
     
 
 
-
-(boris-at-bx.psu.edu)
-
-
 -----
 
 .. class:: infomark
@@ -70,7 +66,7 @@
 
 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 relatives of the minor allele sequence in a NJ tree, the tree plot and newick string.
+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.
 
 -----
 
@@ -79,8 +75,7 @@
 **Note**
 
 This tools DOES NOT align the sequences.
-The FASTA multiple alignment file is fabricated by concatenating same length homologous sequences.
-An independently aligned FASTA multiple alignment file can be used as well.
+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.
 
 -----
 
@@ -88,9 +83,9 @@
 
 **About formats**
 
-**FASTA multiple alignment** -- 
+*FASTA multiple alignment*
 
-describe format shortly
+See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format
 
 -----
 
@@ -104,10 +99,18 @@
     >sample4_major
   
 
-- running this tool with **b = 1000**  **m = yes** **root = RSRS**,  will return::
+- running this tool with *b = 1000*  *m = yes* *root = RSRS*,  will return::
     newick
     relatives
     plot
+
+-----
+
+**Citation**
+
+If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.*
+(boris-at-bx.psu.edu)
+
   </help>
 
 </tool>
\ No newline at end of file