--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/natural_product_likeness_calculator.xml	Thu Aug 15 03:38:29 2013 -0400
@@ -0,0 +1,70 @@
+<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.2.1">
+    <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>
+        ## NPLC is really picky with file extensions. We need to specify every datatype as file extension
+        ## A workaround is to create a symlink with a proper file-extension.
+        #import tempfile
+        #set $temp_file = tempfile.NamedTemporaryFile()
+        #set $temp_link = "%s.%s" % ($temp_file.name, $infile.ext)
+        $temp_file.close()
+        ln -s $infile $temp_link;
+
+        java -jar \$NPLS_JAR_PATH/NP-Likeness-2.0.jar
+            -in "${temp_link}"
+            -out "${outfile}"
+            #if $reconstruct_fragments:
+                -reconstructFragments true
+                -outFragments $outfragments
+            #end if
+        ;
+        rm $temp_link
+    </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_source="infile" 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/
+
+.. image:: $PATH_TO_IMAGES/score_distribution.png
+
+
+-----
+
+.. 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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu Aug 15 03:38:29 2013 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format).">
+    <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>

Binary file static/images/score_distribution.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 15 03:38:29 2013 -0400
@@ -0,0 +1,17 @@
+<tool_dependency>
+    <package name="np-likeness-scorer" version="2.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/np-likeness/Natural_Product_Likeness_calculator_2.0.zip</action>
+               <action type="move_file">
+                    <source>Natural_Product_Likeness_calculator_2.0/NP-Likeness-2.0.jar</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="NPLS_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Opsin requires a JAVA (1.5+) runtime evironment.</readme>
+    </package>
+</tool_dependency>