diff reorder.xml @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

--- a/reorder.xml	Fri Jul 26 12:51:13 2013 -0400
+++ b/reorder.xml	Fri Sep 20 13:25:27 2013 -0400
@@ -1,5 +1,5 @@
-<tool id="gd_reorder" name="Reorder" version="1.0.0">
-  <description>individuals</description>
+<tool id="gd_reorder" name="Reorder individuals" version="1.0.0">
+  <description>: exchange rows in the above picture</description>
 
   <command interpreter="python">
     reorder.py '$input' '$output' '$order'
@@ -15,5 +15,64 @@
   </outputs>
 
   <help>
+**Dataset formats**
+
+The input and output datasets are in gd_indivs_ format.
+
+.. _gd_indivs: ./static/formatHelp.html#gd_indivs
+
+-----
+
+**What it does**
+
+The user picks a gd_indivs dataset from their history and specifies
+a new ordering.  This tool creates a new gd_indivs dataset with the
+individuals reordered as specified by the user.
+
+The new ordering is a list of comma separated ranges (e.g **5,6-12,20**).
+Ranges can be either a single number (e.g. **3**) or two dash separated
+numbers (e.g. **3-5**).  The numbers represent the line number of
+gd_indivs dataset.  Line numbers that are not listed will appear on the
+output after the specified line numbers in their same relative ordering.
+
+-----
+
+**Example**
+
+Input dataset (six rows)::
+
+   18  McClintock
+   22  Peltonen-Palotie
+   26  Sager
+   30  Franklin
+   34  Auerbach
+   38  Stevens
+
+new ordering "**1,3-4**" will return::
+
+   18  McClintock
+   26  Sager
+   30  Franklin
+   22  Peltonen-Palotie
+   34  Auerbach
+   38  Stevens
+
+new ordering "**3,5,1,6**" will return::
+
+   26  Sager
+   34  Auerbach
+   18  McClintock
+   38  Stevens
+   22  Peltonen-Palotie
+   30  Franklin
+
+new ordering "**3-1,6,4-5**" will return::
+
+   26  Sager
+   22  Peltonen-Palotie
+   18  McClintock
+   38  Stevens
+   30  Franklin
+   34  Auerbach
   </help>
 </tool>