# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1370109770 -7200
# Node ID ec87a42dccecd7f2d8aaa3a2d8d29c57fd796bf9
# Parent  5258b01f1f2440f49501d7106bcfc2e5f40c92e9
ChemicalToolBoX update.

diff -r 5258b01f1f24 -r ec87a42dccec convert/ob_convert.xml
--- a/convert/ob_convert.xml	Fri May 31 22:31:31 2013 +0200
+++ b/convert/ob_convert.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -1,8 +1,8 @@
-<tool id="compound_convert" name="Compound Convert" version="0.1">
+<tool id="ctb_compound_convert" name="Compound Convert" version="0.1">
     <description>Converts various chemistry and molecular modeling data files</description>
     <!--<parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
         We can't use that currently, because a few output-datatypes, like the fastsearch index do not support merging. We need to patch galaxy to not abort in such a case
-        and run the job in non.multi mode.
+        and run the job in non-multi mode.
     -->
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>
@@ -251,7 +251,6 @@
             <when value="cssr" />
             <when value="ct" />
             <when value="dmol" />
-            <when value="fa" />
             <when value="fasta" />
             <when value="feat" />
             <when value="fh" />
@@ -285,7 +284,6 @@
             </when>
             <when value="gamin" />
             <when value="gau" />
-            <when value="gjf" />
             <when value="gpr" />
             <when value="gr96" />
             <when value="hin" />
@@ -429,9 +427,16 @@
 
 **What it does**
 
-OpenBabel is a cross-platform program designed to interconvert between many file formats used in molecular modeling and computational chemistry and related areas.
+Interconvert between many file formats used in molecular modeling and computational chemistry and related areas. A few output filetypes provides additional parameters.
+If you are missing some options please contact your administrator or the ChemicalToolBoX team.
+
 
------    
+**References**
+
+N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_
+The Open Babel Package http://openbabel.sourceforge.net/
+
+.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33
 
 
   </help>
diff -r 5258b01f1f24 -r ec87a42dccec filter/multi_obgrep.xml
--- a/filter/multi_obgrep.xml	Fri May 31 22:31:31 2013 +0200
+++ b/filter/multi_obgrep.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -39,7 +39,12 @@
 
 **What it does**
 
-Providing a query file with SMARTS pattern in each line. These tool will run obgreg in parallel and merges the results.
+Providing a query file with SMARTS pattern in each line. These tool will run obgreg_ in parallel and merges the results.
+It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
+
+
+.. _obgrep: http://openbabel.org/wiki/Obgrep
+.. _here: http://openbabel.org/wiki/SMARTS
 
 -----
 
diff -r 5258b01f1f24 -r ec87a42dccec filter/ob_grep.xml
--- a/filter/ob_grep.xml	Fri May 31 22:31:31 2013 +0200
+++ b/filter/ob_grep.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -53,6 +53,11 @@
 **What it does**
 
 The obgrep tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.
+It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
+
+
+.. _obgrep: http://openbabel.org/wiki/Obgrep
+.. _here: http://openbabel.org/wiki/SMARTS
 
 -----
 
@@ -61,8 +66,10 @@
 
 **References**
 
-Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry Rzepa, Christoph Steinbeck, Joerg Kurt Wegner, Egon Willighagen. "The Blue Obelisk -- Interoperability in Chemical Informatics." J. Chem. Inf. Model. (2006) 46(3) 991-998. DOI:10.1021/ci050400b
+N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_
 The Open Babel Package http://openbabel.sourceforge.net/
 
+.. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33
+
     </help>
 </tool>
diff -r 5258b01f1f24 -r ec87a42dccec modify/change_title_to_metadata_value.xml
--- a/modify/change_title_to_metadata_value.xml	Fri May 31 22:31:31 2013 +0200
+++ b/modify/change_title_to_metadata_value.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -2,7 +2,7 @@
     <description>to meta-data value.</description>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
-        <requirement type="python-module">pybel</requirement>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
     </requirements>
     <command interpreter="python">
         ## The command is a Cheetah template which allows some Python based syntax.
diff -r 5258b01f1f24 -r ec87a42dccec modify/ob_addh.xml
--- a/modify/ob_addh.xml	Fri May 31 22:31:31 2013 +0200
+++ b/modify/ob_addh.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="ob_addh" name="Add hydrogen atoms" version="1.0">
+<tool id="ctb_ob_addh" name="Add hydrogen atoms" version="1.0">
     <description>at a certain pH value</description>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
diff -r 5258b01f1f24 -r ec87a42dccec modify/ob_genProp.xml
--- a/modify/ob_genProp.xml	Fri May 31 22:31:31 2013 +0200
+++ b/modify/ob_genProp.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="ob_genProp" name="Compute physico-chemical properties" version="1.0">
+<tool id="ctb_ob_genProp" name="Compute physico-chemical properties" version="1.0">
     <description>for a set of molecules</description>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
     <requirements>
diff -r 5258b01f1f24 -r ec87a42dccec modify/remove_protonation_state.xml
--- a/modify/remove_protonation_state.xml	Fri May 31 22:31:31 2013 +0200
+++ b/modify/remove_protonation_state.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -1,6 +1,9 @@
-<tool id="ctb_remove_protonation_state" name="Remove protonation state">
+<tool id="ctb_remove_protonation_state" name="Remove protonation state" version="0.1">
     <description>of every atom</description>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
     <command interpreter='python'>
     remove_protonation_state.py
         -i $infile
diff -r 5258b01f1f24 -r ec87a42dccec subsearch/subsearch.xml
--- a/subsearch/subsearch.xml	Fri May 31 22:31:31 2013 +0200
+++ b/subsearch/subsearch.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="chemfp_subsearch" name="Substructure Search" version="0.1">
+<tool id="ctb_subsearch" name="Substructure Search" version="0.1">
     <description>of fingerprint data sets</description>
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>
diff -r 5258b01f1f24 -r ec87a42dccec visualisation/ob_depiction_svg.xml
--- a/visualisation/ob_depiction_svg.xml	Fri May 31 22:31:31 2013 +0200
+++ b/visualisation/ob_depiction_svg.xml	Sat Jun 01 20:02:50 2013 +0200
@@ -1,4 +1,4 @@
-<tool id="ob_svg_depiction" name="Visualisation">
+<tool id="ctb_ob_svg_depiction" name="Visualisation">
     <description>of compounds</description>
     <requirements>
         <requirement type="package" version="2.3.2">openbabel</requirement>