comparison align-it.xml @ 1:10c0df29e6d1 draft

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

0:1b8b6787dfbb

<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[

            $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 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>

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

+--------+-----------------------------------------------------------------------+
|   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>

1:10c0df29e6d1

<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[

            $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 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 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>

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

+--------+-----------------------------------------------------------------------+
|   11   | TVERSKY_DB score                                                      |
+--------+-----------------------------------------------------------------------+


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