# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1370109820 -7200
# Node ID fd84ab7af088f0afde2852f59d2ca1ab9b741a37
# Parent  62897185a8038988afc465876fabd98510a362b6
ChemicalToolBoX update.

diff -r 62897185a803 -r fd84ab7af088 align-it/align-it_create_db.xml
--- a/align-it/align-it_create_db.xml	Fri May 31 22:32:15 2013 +0200
+++ b/align-it/align-it_create_db.xml	Sat Jun 01 20:03:40 2013 +0200
@@ -6,11 +6,7 @@
     </requirements>
     <command>
         align-it 
-            #if str($database.ext).strip() == 'phar':
-                --dbType PHAR
-            #else:
-                --dbType MOL
-            #end if
+            --dbType ${database.ext}
             --dbase $database
             --pharmacophore $pharmacophores
             $merge 
@@ -19,7 +15,7 @@
             2>&#38;1
     </command>
     <inputs>
-        <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be converted to pharmacophores" />
+        <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" />
         <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
         <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
     </inputs>
diff -r 62897185a803 -r fd84ab7af088 qed/silicos_qed.xml
--- a/qed/silicos_qed.xml	Fri May 31 22:32:15 2013 +0200
+++ b/qed/silicos_qed.xml	Sat Jun 01 20:03:40 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="silicos_qed" name="Drug-likeness" version="0.1">
+<tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
   <description>quantitative estimation (QED)</description>
   <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
   <requirements>
diff -r 62897185a803 -r fd84ab7af088 strip-it/strip-it.xml
--- a/strip-it/strip-it.xml	Fri May 31 22:32:15 2013 +0200
+++ b/strip-it/strip-it.xml	Sat Jun 01 20:03:40 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="stripit" name="Strip-it" version="1.0.0">
+<tool id="ctb_stripit" name="Strip-it" version="1.0.0">
     <description> extracts predefined scaffolds from molecules</description>
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>