# HG changeset patch
# User bgruening
# Date 1557250867 14400
# Node ID 10c0df29e6d1dc05d4d2afbe3c1fdfefe360a94c
# Parent  1b8b6787dfbbf55ae1076ea0580a4290247f681c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit ed9b6859de648aa5f7cde483732f5df20aaff90e

diff -r 1b8b6787dfbb -r 10c0df29e6d1 align-it.xml
--- a/align-it.xml	Mon May 22 03:02:39 2017 -0400
+++ b/align-it.xml	Tue May 07 13:41:07 2019 -0400
@@ -1,5 +1,5 @@
-<tool id="ctb_alignit" name="Pharmacophore Alignment" version="1.0.3.1">
-    <description>and Optimization (Align-it)</description>
+<tool id="ctb_alignit" name="Pharmacophore alignment" version="1.0.3.1">
+    <description>and optimization (Align-it)</description>
     <requirements>
         <requirement type="package" version="1.0.3">align_it</requirement>
     </requirements>
@@ -54,9 +54,9 @@
     </command>
     <inputs>
         <param name="database" type="data" format='mol,mol2,sdf,smi,txt' label="Defines the database of molecules that will be used to screen"/>
-        <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference Molecule"/>
+        <param name="reference" type="data" format='mol,mol2,sdf,smi,txt' label="Reference molecule"/>
 
-        <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are used in the alignment">
+        <param name="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups to be used in the alignment">
             <option value='AROM' selected="true">aromatic rings</option>
             <option value='HDON' selected="true">hydrogen bond donors</option>
             <option value='HACC' selected="true">hydrogen bond acceptors</option>
@@ -69,30 +69,33 @@
             help="The lower this value, the more strict the matching between two pharmacophores will have to be before they can be aligned.">
             <validator type="in_range" min="0" max="1" />
         </param>
-        <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
+        <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' 
+            help='Reduces computational time by merging neighboring pharmacophore points of the same type'/>
         <param name='noNormal' type='boolean' truevalue='--noNormal' falsevalue='' 
             label='No normal information is included during the alignment'
-            help="Using this flag makes the pharmacophore models less specific but also less conformation-dependent."/>
+            help="Using this flag makes the pharmacophore models less specific, but also less conformation-dependent."/>
         <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."/>
+            label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points, providing a more
+                specific description of the molecule."/>
         <param name='withExclusion' type='boolean' truevalue='--withExclusion' falsevalue=''
             label='Add exclusion spheres into the optimization process instead of processing them afterwards'
-            help="When this flag is set, the exclusion spheres have also an impact on the optimization procedure." />
+            help="When this flag is set, the exclusion spheres also have an impact on the alignment optimization procedure,
+                rather than merely used to calculate the score at the end." />
         <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue=''
-            label='No translational or rotational optimization will be performed' help=""/>
+            label='Skip translational and rotational optimization prior to alignment' help=""/>
 
         <param name='oformat' type='select' format='text' label="The aligned database structures are written to an output file of the following format">
             <option value='smi'>SMILES</option>
             <option value='inchi'>InChI</option>
-            <option value='sdf'>SD file</option>
+            <option value='sdf'>SDF</option>
         </param>
 
         <param name="cutoff" type="float" value="0" label="Only structures with a score larger than this cutoff will be written to the files"
             help="This value should be between 0 and 1.">
             <validator type="in_range" min="0" max="1" />
         </param>
-        <param name="best" type="integer" value="0" label="With this option only a limited number of best scoring structures are written to the files"
-            help="0 means this option is deactivated">
+        <param name="best" type="integer" value="0" label="Maximum number of best scoring structures to write to the files"
+            help="With this option the number of best scoring structures written to the files is limited. 0 means this option is deactivated">
             <validator type="in_range" min="0"/>
         </param>
 
@@ -140,8 +143,10 @@
 The functionality of Align-it_ consists mainly of two parts.
 The first functionality is the generation of pharmacophores from molecules
 (use the tool **Pharmacophore generation** if you want to store these for further use).
-Secondly, pairs of pharmacophores can be aligned (the function of this tool). The resulting
-score is calculated from the volume overlap resulting of the alignments.
+Secondly, the similarity between pairs of pharmacophores can be
+quantified. For this purpose, the pharmacophores need
+to be aligned in three-dimensional space and the overlap volume of the
+alignments calculated.
 
 .. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html
 
@@ -151,7 +156,11 @@
 
 **Input**
 
-* Example::
+Upload a file containing molecular representations in MOL, MOL2, SMILES or
+SDF format; alternatively, if you have already calculated the pharmacophores,
+upload the .phar file containing them.
+
+* Example (SDF)::
 
     - database
 
@@ -224,19 +233,6 @@
 +--------+-----------------------------------------------------------------------+
 
 
-* Example::
-
-    - aligned Pharmacophores
-
-        3033
-        HYBL    -1.98494    1.9958    0.532089    0.7    0    0    0    0
-        HYBL    3.52122    -0.309347    0.122783    0.7    0    0    0    0
-        HYBH    -3.262    -2.9284    -1.0647    1    1    -3.5666    -3.7035    -1.61827
-        HDON    0.2679    -0.2051    -0.399    1    1    -0.076102    -0.981133    -0.927616
-        HACC    -2.7906    -1.9108    0.9092    1    1    -2.74368    -1.94015    1.90767
-        $$$$
-
-
 ]]>
     </help>
     <citations>
diff -r 1b8b6787dfbb -r 10c0df29e6d1 align-it_create_db.xml
--- 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