Mercurial > repos > bgruening > natural_product_likeness

changeset 2:40d181cc8c19 draft

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planemo upload for repository https://github.com/CS76/NP-Likeness commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:33:29 -0400
parents 41e31a198b34
children 6052dd3fa475
files natural_product_likeness_calculator.xml test-data/fragments.sdf
diffstat 2 files changed, 8 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/natural_product_likeness_calculator.xml	Tue May 23 03:09:35 2017 -0400
+++ b/natural_product_likeness_calculator.xml	Tue May 07 13:33:29 2019 -0400
@@ -1,5 +1,5 @@
-<tool id="ctb_np-likeness-calculator" name="Natural Product" version="2.1">
-    <description>likeness calculator</description>
+<tool id="ctb_np-likeness-calculator" name="Natural Product likeness calculator" version="2.1">
+    <description>- calculates the similarity of the molecule to the structure space covered by known natural products</description>
     <requirements>
         <requirement type="package" version="2.1">np-likeness-scorer</requirement>
     </requirements>
@@ -21,7 +21,7 @@
             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' />
+            label='Write out fragments (in SMILES format) and scores?' />
     </inputs>
     <outputs>
         <data format_source="infile" name="outfile" />
@@ -29,10 +29,12 @@
             <filter>reconstruct_fragments is True</filter>
         </data>
     </outputs>
-     <tests>
+    <tests>
         <test>
             <param name="infile" value="CID_3037.sdf"/>
+            <param name="reconstruct_fragments" value="true"/>
             <output name="outfile" file="Score.sdf" ftype="sdf" lines_diff="4"/>
+            <output name="outfragments" file="fragments.sdf" ftype="tabular" compare="contains"/>
         </test>
     </tests>
     <help>
@@ -42,7 +44,7 @@
 
 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 products. The more positive the score, the higher the NP-likeness and vice versa.
 
 .. _Natural-Product-Likeness Scorer: http://sourceforge.net/projects/np-likeness/
 .. image:: $PATH_TO_IMAGES/score_distribution.png
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fragments.sdf	Tue May 07 13:33:29 2019 -0400
@@ -0,0 +1,1 @@
+CC(C)Cl;-01.1053