# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1374244062 -7200
# Node ID 1043c0bb5f777c1b6b7d6b39538d35446613348f
# Parent  955783ed181f8f080643ad8c251603776a8fb4a1
ChemicalToolBoX update.

diff -r 955783ed181f -r 1043c0bb5f77 force_pre-commit_hook_temp_file
diff -r 955783ed181f -r 1043c0bb5f77 get_online_data/get_online_data.xml
--- a/get_online_data/get_online_data.xml	Mon May 27 16:58:49 2013 +0200
+++ b/get_online_data/get_online_data.xml	Fri Jul 19 16:27:42 2013 +0200
@@ -14,7 +14,24 @@
   </outputs>
 
   <help>
-    Fetch data via FTP or HTTP and store them in your history.
-    Supported filetypes are: gz/gzip, rar. ZIP is supported with recurive extracting of specific filetypes.
+
+.. class:: infomark
+
+**What this tool does**
+
+Fetch data via FTP or HTTP and store them in your history.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+Supported filetypes are:
+	- gz/gzip
+	- rar
+
+ZIP is supported with recursive extracting of specific filetypes.
+
   </help>
 </tool>
diff -r 955783ed181f -r 1043c0bb5f77 get_pubchem/get_pubchem_as_smiles.xml
--- a/get_pubchem/get_pubchem_as_smiles.xml	Mon May 27 16:58:49 2013 +0200
+++ b/get_pubchem/get_pubchem_as_smiles.xml	Fri Jul 19 16:27:42 2013 +0200
@@ -15,6 +15,22 @@
   <tests>
   </tests>
   <help>
-  This tool will fetch one pubchem file after another and convert them to a canonical SMILES. The output will be one large SMILES file.
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool will fetch one PubChem_ file after another and convert them to canonical SMILES. 
+
+.. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+The output will be one large SMILES file.
+  
   </help>
 </tool>
diff -r 955783ed181f -r 1043c0bb5f77 jmoleditor/jmoleditor.xml
--- a/jmoleditor/jmoleditor.xml	Mon May 27 16:58:49 2013 +0200
+++ b/jmoleditor/jmoleditor.xml	Fri Jul 19 16:27:42 2013 +0200
@@ -29,10 +29,21 @@
     <options sanitize="False" refresh="True"/>
     <help>
 
-**What it does**
+.. class:: infomark
+
+**What this tool does**
+
+Paint a structure and load it into your Galaxy history.
+
+-----
 
-Paint your strucutre and load it into a Galaxy history.
+.. class:: infomark
+
+**Cite**
 
+Jmol_: an open-source Java viewer for chemical structures in 3D
+
+.. _Jmol: http://jmol.sourceforge.net/
 
     </help>
 </tool>