--- a/natural_product_likeness_calculator.xml	Thu Aug 15 03:38:29 2013 -0400
+++ b/natural_product_likeness_calculator.xml	Tue May 23 03:09:35 2017 -0400
@@ -1,70 +1,56 @@
-<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:: $PATH_TO_IMAGES/score_distribution.png
-
-
------
-
-.. class:: infomark
-
-**Cite**
-
-| KV Jayaseelan, C Steinbeck, P Moreno, A Truszkowski, P Ertl - `Natural product-likeness score revisited: an open-source, open-data implementation`_
-| 
-| P Ertl, S Roggo, and A Schuffenhauer - `Natural product-likeness score and its application for prioritization of compound libraries`_
-
-.. _`Natural product-likeness score revisited: an open-source, open-data implementation`: http://www.biomedcentral.com/1471-2105/13/106/abstract
-.. _`Natural product-likeness score and its application for prioritization of compound libraries`: http://www.ncbi.nlm.nih.gov/pubmed/18034468
-
-    </help>
-</tool>
+<tool id="ctb_np-likeness-calculator" name="Natural Product" version="2.1">
+    <description>likeness calculator</description>
+    <requirements>
+        <requirement type="package" version="2.1">np-likeness-scorer</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+        np-likeness
+            -in '$infile'
+            -intype $infile.ext
+            -out '$outfile'
+            -outtype $infile.ext
+            #if $reconstruct_fragments:
+                -reconstructFragments true
+                -outFragments $outfragments
+            #end if
+    ]]>
+    </command>
+    <inputs>
+        <param format="smi,sdf" name="infile" type="data"
+            label="Molecule file" help="Dataset missing? See TIP below"/>
+        <param name='reconstruct_fragments' type='boolean'
+            truevalue='' falsevalue=''
+            label='Fragments and scores are written out in SMILES format' />
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile" />
+        <data format="tabular" name="outfragments">
+            <filter>reconstruct_fragments is True</filter>
+        </data>
+    </outputs>
+     <tests>
+        <test>
+            <param name="infile" value="CID_3037.sdf"/>
+            <output name="outfile" file="Score.sdf" ftype="sdf" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**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
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/1471-2105-13-106</citation>
+        <citation type="doi">10.1021/ci700286x</citation>
+    </citations>
+</tool>

--- a/repository_dependencies.xml	Thu Aug 15 03:38:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CID_3037.sdf	Tue May 23 03:09:35 2017 -0400
@@ -0,0 +1,220 @@
+3037
+  -OEChem-08231108593D
+
+ 27 28  0     0  0  0  0  0  0999 V2000
+   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1788    2.1664   -0.3787 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0011   -0.0002    1.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2222   -0.2738    0.6597 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2377    0.2772    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2586   -1.3462   -0.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2565    1.3457   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.3343    0.5568    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3322   -0.5574    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4069   -1.5879   -0.9855 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4048    1.5875   -0.9852 C   0  0  0  0  0  0  0  0  0  0  0  0
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+    3.4807   -0.3156    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -3.5190   -0.7571   -0.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.5170    0.7568   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1548    0.8649    2.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1601   -0.8435    2.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.3089    1.3938    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.3053   -1.3909    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -2.4415   -2.4213   -1.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
+    2.4469    2.4191   -1.6835 H   0  0  0  0  0  0  0  0  0  0  0  0
+   -4.4070   -0.9574   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
+    4.4050    0.9570   -1.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.2961   -2.2262    0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3872    2.8487   -1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
+  1 14  1  0  0  0  0
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+ 16 24  1  0  0  0  0
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+M  END
+> <PUBCHEM_COMPOUND_CID>
+3037
+
+> <PUBCHEM_CONFORMER_RMSD>
+0.6
+
+> <PUBCHEM_CONFORMER_DIVERSEORDER>
+8
+10
+12
+1
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+5
+11
+3
+6
+9
+4
+2
+
+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
+25
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+
+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
+2
+
+> <PUBCHEM_PHARMACOPHORE_FEATURES>
+4
+1 3 donor
+1 4 donor
+6 6 8 10 12 14 16 rings
+6 7 9 11 13 15 17 rings
+
+> <PUBCHEM_HEAVY_ATOM_COUNT>
+17
+
+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+5
+
+> <PUBCHEM_CONFORMER_ID>
+00000BDD00000008
+
+> <PUBCHEM_MMFF94_ENERGY>
+44.6858
+
+> <PUBCHEM_FEATURE_SELFOVERLAP>
+20.297
+
+> <PUBCHEM_SHAPE_FINGERPRINT>
+10062212 137 18261117369936506423
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+81228 2 15720767252053392762
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+
+> <PUBCHEM_SHAPE_MULTIPOLES>
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+
+> <PUBCHEM_SHAPE_SELFOVERLAP>
+722.787
+
+> <PUBCHEM_SHAPE_VOLUME>
+193
+
+> <PUBCHEM_COORDINATE_TYPE>
+2
+5
+255
+
+$$$$
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Score.sdf	Tue May 23 03:09:35 2017 -0400
@@ -0,0 +1,139 @@
+3037
+  CDK     0523170409
+
+ 27 28  0  0  0  0  0  0  0  0999 V2000
+   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
+   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
+    0.1788    2.1664   -0.3787 O   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.0011   -0.0002    1.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2222   -0.2738    0.6597 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2377    0.2772    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.2586   -1.3462   -0.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2565    1.3457   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
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+ 16 24  1  0  0  0  0 
+ 17 25  1  0  0  0  0 
+M  END
+> <cdk:Title>
+3037
+
+> <cdk:Remark>
+null
+
+> <PUBCHEM_COMPOUND_CID>
+3037
+
+> <PUBCHEM_CONFORMER_RMSD>
+0.6
+
+> <PUBCHEM_CONFORMER_DIVERSEORDER>
+810121751136942
+
+> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
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+
+> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
+2
+
+> <PUBCHEM_PHARMACOPHORE_FEATURES>
+41 3 donor1 4 donor6 6 8 10 12 14 16 rings6 7 9 11 13 15 17 rings
+
+> <PUBCHEM_HEAVY_ATOM_COUNT>
+17
+
+> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_DEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
+0
+
+> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
+0
+
+> <PUBCHEM_COMPONENT_COUNT>
+1
+
+> <PUBCHEM_CACTVS_TAUTO_COUNT>
+5
+
+> <PUBCHEM_CONFORMER_ID>
+00000BDD00000008
+
+> <PUBCHEM_MMFF94_ENERGY>
+44.6858
+
+> <PUBCHEM_FEATURE_SELFOVERLAP>
+20.297
+
+> <PUBCHEM_SHAPE_FINGERPRINT>
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+
+> <PUBCHEM_SHAPE_MULTIPOLES>
+341.858.381.91.10.020-1.151.94-0.010-0.39-4.150.010
+
+> <PUBCHEM_SHAPE_SELFOVERLAP>
+722.787
+
+> <PUBCHEM_SHAPE_VOLUME>
+193
+
+> <PUBCHEM_COORDINATE_TYPE>
+25255
+
+> <NATURAL_PRODUCT_LIKENESS_SCORE>
+-00.1511
+
+> <UNIQUE_MOLECULE_ID>
+eb878dfc-1074-456a-ab86-c7fc4f84bf2a
+
+$$$$

--- a/tool_dependencies.xml	Thu Aug 15 03:38:29 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-<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>