annotate align-it.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" name="Pharmacophore alignment" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>and optimization (Align-it)</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.4</token>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">align_it</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
        align-it
            #if str($database.ext).strip() == 'phar':
                --dbType PHAR
            #else:
                --dbType '${database.ext}'
            #end if
            --dbase "$database"

            --reference "$reference"
            #if str($reference.ext).strip() == 'phar':
                --refType PHAR
            #else:
                --refType ${reference.ext}
            #end if
            #######################################
            #### output options
            #######################################
            --pharmacophore $aligned_pharmacophores


            --out '$aligned_structures'
            --outType $oformat

            #if float( str($cutoff) ) > 0:
                --cutOff $cutoff
            #end if
            #if int( str($best) ) > 0:
                --best $best
            #end if
            --rankBy $rankBy
            --scores '$score_result_file'

            #######################################
            #### Options
            #######################################

            #set $fgroups_combined = str( $fgroups ).strip()
            --funcGroup $fgroups_combined

            --epsilon $epsilon
            $merge
            $noNormal
            $noHybrid
            $scoreOnly
            $withExclusion
]]>
    </command>
    <inputs>
        <param name="database" type="data" format='mol,mol2,sdf,smi,phar' label="Defines the database of molecules that will be used to screen"/>
        <param name="reference" type="data" format='mol,mol2,sdf,smi,phar' label="Reference molecule"/>

        <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>
            <option value='LIPO' selected="true">lipophilic spots</option>
            <option value='CHARGE' selected="true">charge centers</option>
        </param>


        <param name="epsilon" type="float" value="0.5" label='Change the tolerance for points to be matched in the alignment phase'
            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' 
            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."/>
        <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."/>
        <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 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='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'>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="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>

        <param name='rankBy' type='select' format='text' label="This option defines the used scoring scheme">
            <option value='TANIMOTO'>Tanimoto</option>
            <option value='TVERSKY_REF'>TVERSKY_REF</option>
            <option value='TVERSKY_DB'>TVERSKY_DB</option>
        </param>

    </inputs>
    <outputs>
        <data name="aligned_pharmacophores" format="phar" label="${tool.name} on ${on_string} (aligned pharmacophores)"/>
        <data name="aligned_structures" format="smi" label="${tool.name} on ${on_string} (aligned structures)">
            <change_format>
                <when input="oformat" value="inchi" format="inchi"/>
                <when input="oformat" value="sdf" format="sdf"/>
            </change_format>
        </data>
        <data name="score_result_file" format="tabular" label="${tool.name} on ${on_string} (scores)"/>
    </outputs>
    <tests>
        <test>
            <param name="database" ftype="sdf" value="CID_2244.sdf"/>
            <param name="reference" ftype="sdf" value="CID_2244.sdf"/>
            <param name="oformat" value="sdf"/>
            <output name="aligned_pharmacophores" file="align-it_Search_on_CID2244.phar" ftype="phar" />
            <output name="aligned_structures" file="align-it_Search_on_CID2244.sdf" lines_diff="2" />
            <output name="score_result_file" file="aliginit_scores.tabular.tabular" />
        </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.
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
(use the tool **Pharmacophore generation** if you want to store these for further use).
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

-----

.. class:: infomark

**Input**

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

     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**

The format of the output file is shown in the table below:

+--------+-----------------------------------------------------------------------+
| Column |                           Content                                     |
+========+=======================================================================+
|    1   | Id of the reference structure                                         |
+--------+-----------------------------------------------------------------------+
|    2   | Maximum volume of the reference structure                             |
+--------+-----------------------------------------------------------------------+
|    3   | Id of the database structure                                          |
+--------+-----------------------------------------------------------------------+
|    4   | Maximum volume of the database structure                              |
+--------+-----------------------------------------------------------------------+
|    5   | Maximum volume overlap of the two structures                          |
+--------+-----------------------------------------------------------------------+
|    6   | Overlap between pharmacophore and exclusion spheres in the reference  |
+--------+-----------------------------------------------------------------------+
|    7   | Corrected volume overlap between database pharmacophore and reference |
+--------+-----------------------------------------------------------------------+
|    8   | Number of pharmacophore points in the processed pharmacophore         |
+--------+-----------------------------------------------------------------------+
|    9   | TANIMOTO score                                                        |
+--------+-----------------------------------------------------------------------+
|   10   | TVERSKY_REF score                                                     |
+--------+-----------------------------------------------------------------------+
|   11   | TVERSKY_DB score                                                      |
+--------+-----------------------------------------------------------------------+


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