changeset 0:efba95c2ca20

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/natural_product_likeness_calculator.xml	Fri Apr 26 08:41:39 2013 -0400
@@ -0,0 +1,63 @@
+<tool id="ctb_np-likeness-calculator" name="Natural Product" version="0.1">
+    <description>likeness calculator</description>
+    <requirements>
+        <requirement type="package" version="1.4.1">np-likeness-scorer</requirement>
+    </requirements>
+    <command>
+        java -jar \$JAVA_JAR_PATH/NPLikenessCalculator-1.4.1.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="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
+
+**INFO:** The more positive the score, the higher is the NP-likeness and vice versa.
+
+.. image:: $PATH_TO_IMAGES/score_distribution.png
+
+
+**What it is**
+
+The `Natural-Product-Likeness Scorer`_ is an open-source, open-data re-implementation of 
+Peter Ertl’s previous work [2] and calculates a natural product-likeness score.
+
+.. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/
+
+-----
+
+    
+**Cite**
+[1] KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl, Natural product-likeness score revisited:
+an open-source, open-data implementation, BMC Bioinformatics 2012, 13:106
+
+http://www.biomedcentral.com/1471-2105/13/106/abstract
+
+[2] P Ertl, S Roggo, and A Schuffenhauer, Natural product-likeness score and its application for prioritization
+of compound libraries., J. Chem. Inf. Model, 2008 vol. 48 (1) pp. 68-74
+
+http://www.ncbi.nlm.nih.gov/pubmed/18034468
+
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Fri Apr 26 08:41:39 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 toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="25698453d7d7" />
+</repositories> 

Binary file static/images/score_distribution.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Apr 26 08:41:39 2013 -0400
@@ -0,0 +1,17 @@
+<tool_dependency>
+    <package name="np-likeness-scorer" version="1.4.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/np-likeness/Natural%20Product%20Likeness%20calculator%201.4.1.zip</action>
+               <action type="move_file">
+                    <source>Natural Product Likeness calculator 1.4.1/NPLikenessCalculator-1.4.1.jar</source>
+                    <destination>$INSTALL_DIR/jars</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Opsin requires a JAVA (1.5+) runtime evironment.</readme>
+    </package>
+</tool_dependency>