changeset 1:b8809b15e1a4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e

--- a/strip-it.xml	Mon May 22 03:01:21 2017 -0400
+++ b/strip-it.xml	Tue May 07 13:42:01 2019 -0400
@@ -1,5 +1,5 @@
 <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
-    <description>extracts predefined scaffolds from molecules</description>
+    <description>extracts scaffolds from molecules</description>
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <requirements>
         <requirement type="package" version="1.0.2">strip_it</requirement>
@@ -38,11 +38,8 @@
 
 **What this tool does**
 
-Strip-it is a program that extracts predefined scaffolds from organic small
-molecules.
-
-The program comes with a number of predefined molecular scaffolds for
-extraction. These scaffolds include, amongst others
+Strip-it is a program that extracts scaffolds from organic small molecules, 
+based on predefined scaffold types. The scaffold types used by Strip-it include
 
     - `molecular frameworks`_ as originally described by Bemis and Murcko
     - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
@@ -59,13 +56,13 @@
 
 **Input**
 
-| - `SD-Format`_
-| - `SMILES Format`_
-| - `MOL2 Format`_
+| - `SDF format`_
+| - `SMILES format`_
+| - `MOL2 format`_
 
-.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
-.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
-.. _MOL2 Format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
+.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+.. _MOL2 format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
 
 
 -----
@@ -74,6 +71,9 @@
 
 **Output**
 
+A tabular file with the name and SMILES of the molecule in the first two 
+columns; subsequent columns show scaffolds extracted by different methods.
+
 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
 |     NAME    |            MOLECULE            | RINGS_WITH_LINKERS_1 |  RINGS_WITH_LINKERS_2  |       MURCKO_1       | ... |
 +=============+================================+======================+========================+======================+=====+
@@ -98,5 +98,11 @@
 ]]>
     </help>
     <citations>
+        <citation type="bibtex">@misc{
+            title={Strip-it},
+            author={Silicos-it},
+            year={2014},
+
+        }</citation>
     </citations>
 </tool>