annotate align-it_create_db.xml @ 2:06d9381593a4 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit 00844534f9a2ffdf41fb9d5186d9a1e574c302d2"

<tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1">
    <description>generation (Align-it)</description>
    <requirements>
        <requirement type="package" version="1.0.3">align_it</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
        align-it
            --dbType '${database.ext}'
            --dbase '$database'
            --pharmacophore '$pharmacophores'
            $merge
            $noHybrid
]]>
    </command>
    <inputs>
        <param name="database" type="data" format='mol,mol2,sdf,smi'
            label="Defines the database of molecules that will be converted to pharmacophores" />
        <param name='merge' type='boolean' truevalue='--merge' falsevalue=''
            label='Merge pharmacophore points' 
            help='Reduces computational time by merging neighboring pharmacophore points of the same type'/>
        <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue=''
            label='Disable the use of hybrid pharmacophore points'
            help="Using this flag will increase the number of pharmacophore points, providing a more
                specific description of the molecule"/>
    </inputs>
    <outputs>
        <data name="pharmacophores" format="txt" label="${tool.name} on ${on_string} (scores)"/>
    </outputs>
    <tests>
        <test>
            <param name="database" ftype="sdf" value="6mol.sdf"/>
            <output name="pharmacophores" file="alignit_Create_Phar_DB_6mol.phar" />
        </test>
    </tests>
    <help>
<![CDATA[

.. class:: infomark

**What this tool does**

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. 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.

The functionality of Align-it_ consists mainly of two parts.
The first functionality is the generation of pharmacophores from molecules
(the function of this tool). Secondly, pairs of pharmacophores
can be aligned (use the tool **Pharmacophore Alignment**). The resulting
score is calculated from the volume overlap resulting of the alignments.

.. _Align-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html

-----

.. class:: infomark

**Input**

Upload a file containing molecular representations in MOL, MOL2, SMILES or
SDF format.

* Example (SDF)::

    - database

     30 31  0     0  0  0  0  0  0999 V2000
        1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
        1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
       -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
       -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
        0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
       -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
       -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
       -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
        1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
       -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
       -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
       -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
       -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
        2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
        2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
       -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
        3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
        3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
        4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
       -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
       -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
       -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
       -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
        0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
       -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
       -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
        4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
        3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
        5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
       -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0

    - cutoff : 0.0

-----

.. class:: infomark

**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

        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>
        <citation type="doi">10.1016/j.jmgm.2008.04.003</citation>
    </citations>
</tool>