# HG changeset patch
# User Bjoern Gruening <bjoern.gruening@gmail.com>
# Date 1374333979 -7200
# Node ID 63f87ebdeb8e36e009188831067d96739f7e9b97
# Parent  08e8e01c6fcb8298e11248b740ec6311cb12acc1
ChemicalToolBoX update.

diff -r 08e8e01c6fcb -r 63f87ebdeb8e natural_product_likeness_calculator.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/natural_product_likeness_calculator.xml.orig	Sat Jul 20 17:26:19 2013 +0200
@@ -0,0 +1,65 @@
+<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.2">
+    <description>likeness calculator</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,outfragments"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.0">np-likeness-scorer</requirement>
+    </requirements>
+    <command>
+        java -jar \$NPLS_JAR_PATH/NP-Likeness-2.0.jar
+            -in "${infile}"
+            -out "${outfile}"
+            #if $reconstruct_fragments:
+                -reconstructFragments true
+                -outFragments $outfragments
+            #end if
+    </command>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param format="smi,sdf" name="infile" type="data" label="Molecule file" help="Dataset missing? See TIP below"/>
+        <param name='reconstruct_fragments' type='boolean' label='Fragments-scores are written out in SMILES format' truevalue='' falsevalue='' />
+    </inputs>
+    <outputs>
+        <data format="sdf" name="outfile" />
+        <data format="tabular" name="outfragments">
+            <filter>reconstruct_fragments is True</filter>
+        </data>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+
+
+.. class:: infomark
+
+**What this tool does**
+
+The `Natural-Product-Likeness Scorer`_ calculates the Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. The more positive the score, the higher is the NP-likeness and vice versa.
+
+.. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/
+
+<<<<<<< HEAD
+The `Natural-Product-Likeness Scorer`_ is an open-source, open-data re-implementation of 
+Peter Ertls previous work [2] and calculates a natural product-likeness score.
+=======
+.. image:: $PATH_TO_IMAGES/score_distribution.png
+>>>>>>> 67ce87e8ccf30f81f72248a7fde0896c5e9ae953
+
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+| KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl - `Natural product-likeness score revisited: an open-source, open-data implementation`_
+| 
+| P Ertl, S Roggo, and A Schuffenhauer - `Natural product-likeness score and its application for prioritization of compound libraries`_
+
+.. _`Natural product-likeness score revisited: an open-source, open-data implementation`: http://www.biomedcentral.com/1471-2105/13/106/abstract
+.. _`Natural product-likeness score and its application for prioritization of compound libraries`: http://www.ncbi.nlm.nih.gov/pubmed/18034468
+
+    </help>
+</tool>