diff align-it_create_db.xml @ 1:10c0df29e6d1 draft

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

--- a/align-it_create_db.xml	Mon May 22 03:02:39 2017 -0400
+++ b/align-it_create_db.xml	Tue May 07 13:41:07 2019 -0400
@@ -17,10 +17,12 @@
         <param name="database" type="data" format='mol,mol2,sdf,smi'
             label="Defines the database of molecules that will be converted to pharmacophores" />
         <param name='merge' type='boolean' truevalue='--merge' falsevalue=''
-            label='Merge pharmacophore points' />
+            label='Merge pharmacophore points' 
+            help='Reduces computational time by merging neighboring pharmacophore points of the same type'/>
         <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue=''
             label='Disable the use of hybrid pharmacophore points'
-            help="Using this flag will increase the number of pharmacophore points."/>
+            help="Using this flag will increase the number of pharmacophore points, providing a more
+                specific description of the molecule"/>
     </inputs>
     <outputs>
         <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/>
@@ -41,7 +43,9 @@
 Align-it_ is a tool to align molecules according to their pharmacophores.
 A pharmacophore is an abstract concept based on the specific interactions
 observed in drug-receptor interactions: hydrogen bonding,
-charge transfer, electrostatic and hydrophobic interactions.
+charge transfer, electrostatic and hydrophobic interactions. Each pharmacophore
+contains multiple lines, representing so-called pharmacophore
+points, each of which corresponds to a functional group of the molecule.
 Molecular modeling and/or screening based on pharmacophore similarities
 has been proven to be an important and useful method in drug discovery.
 
@@ -51,7 +55,7 @@
 can be aligned (use the tool **Pharmacophore Alignment**). The resulting
 score is calculated from the volume overlap resulting of the alignments.
 
-.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html
+.. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
 
 -----
 
@@ -59,7 +63,10 @@
 
 **Input**
 
-* Example::
+Upload a file containing molecular representations in MOL, MOL2, SMILES or
+SDF format.
+
+* Example (SDF)::
 
     - database
 
@@ -103,6 +110,14 @@
 
 **Output**
 
+A series of lines for each molecule, each describing a pharmocophore point
+(functional group) of the molecules. The first column specifies a functional
+type (e.g. HACC is a hydrogen bond acceptor; HYBL is a aromatic, lipophilic
+region). Subsequent columns specify the position of the center in three-dimensional
+space; see the documentation_ for more details.
+
+.. _documentation: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
+
 * Example::
 
     - aligned Pharmacophores