--- a/shape-it.xml	Mon May 22 03:02:57 2017 -0400
+++ b/shape-it.xml	Tue May 07 13:41:43 2019 -0400
@@ -1,5 +1,5 @@
 <tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0">
-    <description>Against a database of molecules (shape-it)</description>
+    <description>against a database of molecules (shape-it)</description>
     <requirements>
         <requirement type="package" version="1.0.1">shape_it</requirement>
     </requirements>
@@ -31,20 +31,20 @@
 ]]>
     </command>
     <inputs>
-        <param name="reference" type="data" format='sdf,mol,mol2' label="Refrence molecule (with 3D coordinates)" />
+        <param name="reference" type="data" format='sdf,mol,mol2' label="Reference molecule (with 3D coordinates)" />
         <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
-        <param name="cutoff" type="float" value="0.0" label="Only molecules with a score higher than the cutoff are reported."
-            help="The scoring function is defined by the scoring scheme.">
+        <param name="cutoff" type="float" value="0.0" label="Cutoff"
+            help="Only molecules with a score higher than the cutoff are reported; the scoring function is defined by the scoring scheme.">
             <validator type="in_range" min="0.0" />
         </param>
         <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure'
             help="The default value is set to 0, which refers to only a local gradient ascent."/>
-        <param name='best' type='integer' value='0' label='The N best scoring molecules are reported' help="0 means all molecules are reported"/>
-        <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a Tab-delimited text file with the scores of molecules' checked="false" />
-        <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='The reference molecule is not written into the output files' checked="false" />
+        <param name='best' type='integer' value='0' label='Number of best-scoring molecules to report' help="The N best scoring molecules are reported; 0 means all molecules are reported"/>
+        <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a tab-delimited text file with the molecule scores' checked="false" />
+        <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='Do not write reference molecule into the output files' checked="false" />
         <param name='scoreonly' type='boolean' truevalue='--scoreOnly' falsevalue=''
             label='Only the volume overlap between the reference and the given pose is computed' checked="false" />
-        <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
+        <param name='rankBy' type='select' format='text' label="Scoring scheme">
             <option value='TANIMOTO'>Tanimoto</option>
             <option value='TVERSKY_REF'>TVERSKY_REF</option>
             <option value='TVERSKY_DB'>TVERSKY_DB</option>
@@ -76,8 +76,8 @@
 **What this tool does**
 
 Shape-it_ is a tool that aligns a reference molecule against a set of database
-molecules using the shape of the molecules as the align criterion.
-It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as it was introduced by Grant and Pickup.
+molecules using the shape of the molecules as the alignment criterion.
+It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as was introduced by Grant and Pickup.
 
 The program expects one reference molecule with
 its three-dimensional coordinates and one database files containing one
@@ -95,11 +95,11 @@
 **Input**
 
 
-| - `formates recognized by OpenBabel`_
+`3D formats recognized by OpenBabel`_ - either SDF, MOL, or MOL2
 
-.. _formates recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
+.. _3D formats recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats
 
-* Example::
+* Example (SDF)::
 
 	- database
 		27 28  0     0  0  0  0  0  0999 V2000
@@ -193,6 +193,11 @@
 
 **Output**
 
+The output file contains first the reference molecule, followed by the molecules 
+aligned to the reference molecule. If the 'Number of best-scoring molecules' option
+is set only the top-best scoring molecules will be reported in the output file,
+otherwise all molecules are written to the output file.
+
 * Example::
 
 	 27 28  0  0  0  0  0  0  0  0999 V2000
@@ -236,6 +241,16 @@
 	  6  8  2  0  0  0  0
 	  ......
 
+In addition, if the option to output scores is selected, a tabular file will be created.
+Each line represents a molecule from the database, with columns describing the volumes 
+of the reference and database molecules, overlap volumes, and Shape-it scores produced 
+by the three scoring schemes.
+
+* Example::
+
+	dbName  refName Shape-it::Tanimoto      Shape-it::Tversky_Ref   Shape-it::Tversky_Db    overlap refVolume       dbVolume
+	3033    3037    0.562                   0.754                   0.688                   128.56  169.59          187.87
+
 
 ]]>
     </help>