annotate align-it.xml @ 0:1b8b6787dfbb draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/align-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7

<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>
    <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,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="fgroups" type="select" multiple="True" display="checkboxes" label="Specify a subset of the available functional groups that are 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' />
        <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."/>
        <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." />
        <param name='scoreOnly' type='boolean' truevalue='--scoreOnly' falsevalue=''
            label='No translational or rotational optimization will be performed' 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>
        </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">
            <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="txt" 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" />
            <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, pairs of pharmacophores can be aligned (the function of this tool). 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**

* Example::

    - 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                                                      |
+--------+-----------------------------------------------------------------------+


* 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>