# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1370195667 -7200
# Node ID 588e3ff42c28af7582a1472b0e1751d6780277d2
# Parent  fd84ab7af088f0afde2852f59d2ca1ab9b741a37
ChemicalToolBoX update.

diff -r fd84ab7af088 -r 588e3ff42c28 align-it/align-it.xml
--- a/align-it/align-it.xml	Sat Jun 01 20:03:40 2013 +0200
+++ b/align-it/align-it.xml	Sun Jun 02 19:54:27 2013 +0200
@@ -9,7 +9,7 @@
             #if str($database.ext).strip() == 'phar':
                 --dbType PHAR
             #else:
-                --dbType MOL
+                --dbType ${database.ext}
             #end if
             --dbase $database
 
@@ -17,7 +17,7 @@
             #if str($reference.ext).strip() == 'phar':
                 --refType PHAR
             #else:
-                --refType MOL
+                --refType ${reference.ext}
             #end if
             #######################################
             #### output options
@@ -123,9 +123,9 @@
 have proven to be an important and useful method in drug discovery.
 
 The functionality of Align-it_ consists mainly of two parts. 
-The first functionality consists of the **generation of pharmacophores from molecules** 
+The first functionality consists of the generation of pharmacophores from molecules 
 (use the tool *Pharmacophore generation* if you want to store these for later use).
-Second, pairs of pharmacophores can be aligned and the resulting 
+Second, pairs of **pharmacophores can be aligned** and the resulting 
 score is calculated from the volume overlap resulting from the alignments.
 
 
diff -r fd84ab7af088 -r 588e3ff42c28 align-it/align-it_create_db.xml
--- a/align-it/align-it_create_db.xml	Sat Jun 01 20:03:40 2013 +0200
+++ b/align-it/align-it_create_db.xml	Sun Jun 02 19:54:27 2013 +0200
@@ -39,7 +39,7 @@
 
 The functionality of Align-it_ consists mainly of two parts. 
 The first functionality consists of the **generation of pharmacophores from molecules** 
-(thats the function of this tool). Second, pairs of pharmacophores 
+(the function of this tool). Second, pairs of pharmacophores 
 can be aligned (use the tool *Pharmacophore Alignment*) and the resulting 
 score is calculated from the volume overlap resulting from the alignments.
 
diff -r fd84ab7af088 -r 588e3ff42c28 shape-it/shape-it.xml
--- a/shape-it/shape-it.xml	Sat Jun 01 20:03:40 2013 +0200
+++ b/shape-it/shape-it.xml	Sun Jun 02 19:54:27 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="shapeit" name="Shape alignment" version="0.1">
+<tool id="ctb_shapeit" name="Shape alignment" version="0.1">
     <description>against a database of molecules (Shape-it)</description>
     <requirements>
         <requirement type="package" version="1.0.0">silicos_it</requirement>