# HG changeset patch
# User boris
# Date 1372135846 14400
# Node ID 479f860eb8a9c5d639f2e4cfee676f9e7ef254f0
# Parent  57c5ea9c3c5c89c7c7cc86c279527ce638e114f6
updated tool xml description

diff -r 57c5ea9c3c5c -r 479f860eb8a9 hetbox.xml
--- a/hetbox.xml	Fri Jun 21 16:05:46 2013 -0400
+++ b/hetbox.xml	Tue Jun 25 00:50:46 2013 -0400
@@ -1,5 +1,5 @@
-<tool id="hetbox" version="1.0" name="Minor variant boxplot">
-  <description> from allele counts</description>
+<tool id="hetbox" version="1.0" name="MAF boxplot">
+  <description></description>
   <requirements>
     <requirement type="package" version="2.15.0">R</requirement>
     <requirement type="package" version="2.2.6">rpy2</requirement>
@@ -8,12 +8,12 @@
   <command interpreter="python">hetbox.py $input $outplot $outreport
   </command>
   <inputs>
-    <param name="input" type="data" format="tabular" label="Input allele counts"/>
-    <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also produce a potential contamination report" />
+    <param name="input" type="data" format="tabular" label="Input allele counts table"/>
+    <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also generate a report on data spread" />
   </inputs>
   <outputs>
-    <data name="outplot" format="png"/>
-    <data name="outreport" format="tabular">
+    <data name="outplot" format="png" label="${tool.name} on ${on_string}: boxplot"/>
+    <data name="outreport" format="tabular" label="${tool.name} on ${on_string}: report">
       <filter>report is True</filter>
     </data>
   </outputs>
@@ -28,19 +28,47 @@
 
 **What it does**
 
-Given a table with sample ids and minor alelles frequencies, generates boxplot per sample and 
+The MAF Boxplot tool takes a table listing heteroplasmic sites per sample and their corresponding minor allele frequency.
+It generates a boxplot of the minor allele frequencies per sample by default. 
+Optionally, it can generate  a report including the total number of heteroplasmic sites and the median and the median absolute deviation (MAD) of the minor allele frequencies per sample.
+
+-----
+
+.. class:: warningmark
+
+**Note**
+
+Please, follow the format described below for the input file:
+
+-----
 
 .. class:: infomark
 
-**Boxplot**
+**Formats**
 
-The graphic shows the distribution of the minor allele frequencies as a boxplot per sample. At the bottom of each plot, a count (N) is given of the number of minor alleles in the plot.
+**Count alleles tool output format**
 
+Columns::
 
-**Report**
+    1.  sample id
+    2.  chromosome
+    3.  position
+    4   counts for A's
+    5.  counts for C's
+    6.  counts for G's
+    7.  counts for T's
+    8.  Coverage
+    9.  Number of alleles passing frequency threshold
+    10. Major allele
+    11. Minor allele
+    12. Minor allele frequency in position
 
-The graphic shows the distribution of the minor allele frequencies as a boxplot per sample. At the bottom of each plot, a count (N) is given of the number of minor alleles in the plot.
+-----
 
+**Citation**
+
+If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.*
+(boris-at-bx.psu.edu)
 
 
   </help>