annotate shape-it.xml @ 1:d7ecb50b2b66 draft default tip

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

<tool id="ctb_shapeit" name="Shape alignment" version="1.0.1.0">
    <description>against a database of molecules (shape-it)</description>
    <requirements>
        <requirement type="package" version="1.0.1">shape_it</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[

    ln -s ${database} ./database.${database.ext} &&
    ln -s ${reference} ./reference.${reference.ext} &&

    shape-it
        --format ${database.ext}
        --dbase ./database.${database.ext}
        --reference ./reference.${reference.ext}
        --addIterations $addIterations
        #if int($best) > 0:
            --best $best
        #end if
        --cutoff $cutoff
        #if $scores:
            --scores $output_scores
        #end if
        --rankBy $rankBy
        $noref
        $scoreonly
        --out ./result.${database.ext}
        
        &&
        mv ./result.${database.ext} '$output'
]]>
    </command>
    <inputs>
        <param name="reference" type="data" format='sdf,mol,mol2' label="Reference molecule (with 3D coordinates)" />
        <param name="database" type="data" format='sdf,mol,mol2' label="Database of molecules (with 3D coordinates)" />
        <param name="cutoff" type="float" value="0.0" label="Cutoff"
            help="Only molecules with a score higher than the cutoff are reported; the scoring function is defined by the scoring scheme.">
            <validator type="in_range" min="0.0" />
        </param>
        <param name='addIterations' type='integer' value='0' label='Perform N additional optimization steps with the simulated annealing procedure'
            help="The default value is set to 0, which refers to only a local gradient ascent."/>
        <param name='best' type='integer' value='0' label='Number of best-scoring molecules to report' help="The N best scoring molecules are reported; 0 means all molecules are reported"/>
        <param name='scores' type='boolean' truevalue='yes' falsevalue='' label='Output a tab-delimited text file with the molecule scores' checked="false" />
        <param name='noref' type='boolean' truevalue='--noRef' falsevalue='' label='Do not write reference molecule into the output files' checked="false" />
        <param name='scoreonly' type='boolean' truevalue='--scoreOnly' falsevalue=''
            label='Only the volume overlap between the reference and the given pose is computed' checked="false" />
        <param name='rankBy' type='select' format='text' label="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="output" format_source='database' />
        <data name="output_scores" format="tabular">
            <filter>scores is True</filter>
         </data>
    </outputs>
    <tests>
        <test>
            <param name="database" ftype='sdf' value="CID_3033.sdf" />
            <param name="reference" ftype="sdf" value='CID_3037.sdf' />
            <param name="cutoff" value="0.0" />
            <param name='addIterations' value='0' />
            <param name='best' value='0' />
            <param name='scoreonly' value="true" />
            <output name="output" ftype='sdf' file="shapeit_on_CID3033_and_CID3037.sdf" lines_diff="4" />
        </test>
    </tests>
    <help>
<![CDATA[


.. class:: infomark

**What this tool does**

Shape-it_ is a tool that aligns a reference molecule against a set of database
molecules using the shape of the molecules as the alignment criterion.
It is based on the use of `gaussian volumes as descriptor for molecular shape`_ as was introduced by Grant and Pickup.

The program expects one reference molecule with
its three-dimensional coordinates and one database files containing one
or more molecules in three dimensions. The results are either the alignment
of all database molecules and their respective scores or the N best
scoring molecules of the complete database.

.. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
.. _Shape-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/shape-it/1.0.1/shape-it.html

-----

.. class:: infomark

**Input**


`3D formats recognized by OpenBabel`_ - either SDF, MOL, or MOL2

.. _3D formats recognized by OpenBabel: http://openbabel.org/wiki/Category:Formats

* Example (SDF)::

	- database
		27 28  0     0  0  0  0  0  0999 V2000
	   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
	    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
	   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
	    0.1788    2.1664   -0.3787 O   0  0  0  0  0  0  0  0  0  0  0  0
	   -0.0011   -0.0002    1.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -1.2222   -0.2738    0.6597 C   0  0  0  0  0  0  0  0  0  0  0  0
	    1.2377    0.2772    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -1.2586   -1.3462   -0.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
	    1.2565    1.3457   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.3343    0.5568    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
	    2.3322   -0.5574    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.4069   -1.5879   -0.9855 C   0  0  0  0  0  0  0  0  0  0  0  0
	    2.4048    1.5875   -0.9852 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -3.4827    0.3152    0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
	    3.4807   -0.3156    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -3.5190   -0.7571   -0.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
	    3.5170    0.7568   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -0.1548    0.8649    2.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.1601   -0.8435    2.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.3089    1.3938    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
	    2.3053   -1.3909    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.4415   -2.4213   -1.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
	    2.4469    2.4191   -1.6835 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -4.4070   -0.9574   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
	    4.4050    0.9570   -1.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.2961   -2.2262    0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.3872    2.8487   -1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
	  1 14  1  0  0  0  0
	  2 15  1  0  0  0  0
	  3  8  1  0  0  0  0
	  3 26  1  0  0  0  0
	  4  9  1  0  0  0  0
	  4 27  1  0  0  0  0
	  5  6  1  0  0  0  0
	  5  7  1  0  0  0  0
	  .....

	- reference

		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
	  1 14  1  0  0  0  0
	  2 15  1  0  0  0  0
	  3 16  1  0  0  0  0
	  3 30  1  0  0  0  0
	  4 16  2  0  0  0  0
	  5  7  1  0  0  0  0
	  5  9  1  0  0  0  0
	  5 22  1  0  0  0  0
	  6  7  1  0  0  0  0
	  6  8  1  0  0  0  0
	  ......

	- cutoff : 0.0

-----

.. class:: infomark

**Output**

The output file contains first the reference molecule, followed by the molecules 
aligned to the reference molecule. If the 'Number of best-scoring molecules' option
is set only the top-best scoring molecules will be reported in the output file,
otherwise all molecules are written to the output file.

* Example::

	 27 28  0  0  0  0  0  0  0  0999 V2000
	   -4.8550    1.3401    0.2120 Cl  0  0  0  0  0  0  0  0  0  0  0  0
	    4.8529   -1.3406    0.2121 Cl  0  0  0  0  0  0  0  0  0  0  0  0
	   -0.1809   -2.1668   -0.3789 O   0  0  0  0  0  0  0  0  0  0  0  0
	    0.1788    2.1664   -0.3787 O   0  0  0  0  0  0  0  0  0  0  0  0
	   -0.0011   -0.0002    1.4744 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -1.2222   -0.2738    0.6597 C   0  0  0  0  0  0  0  0  0  0  0  0
	    1.2377    0.2772    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -1.2586   -1.3462   -0.2316 C   0  0  0  0  0  0  0  0  0  0  0  0
	    1.2565    1.3457   -0.2314 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.3343    0.5568    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
	    2.3322   -0.5574    0.7972 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.4069   -1.5879   -0.9855 C   0  0  0  0  0  0  0  0  0  0  0  0
	    2.4048    1.5875   -0.9852 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -3.4827    0.3152    0.0433 C   0  0  0  0  0  0  0  0  0  0  0  0
	    3.4807   -0.3156    0.0435 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -3.5190   -0.7571   -0.8481 C   0  0  0  0  0  0  0  0  0  0  0  0
	    3.5170    0.7568   -0.8478 C   0  0  0  0  0  0  0  0  0  0  0  0
	   -0.1548    0.8649    2.1342 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.1601   -0.8435    2.1593 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.3089    1.3938    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
	    2.3053   -1.3909    1.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -2.4415   -2.4213   -1.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
	    2.4469    2.4191   -1.6835 H   0  0  0  0  0  0  0  0  0  0  0  0
	   -4.4070   -0.9574   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
	    4.4050    0.9570   -1.4418 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.2961   -2.2262    0.4641 H   0  0  0  0  0  0  0  0  0  0  0  0
	    0.3872    2.8487   -1.0397 H   0  0  0  0  0  0  0  0  0  0  0  0
	  1 14  1  0  0  0  0
	  2 15  1  0  0  0  0
	  3  8  1  0  0  0  0
	  3 26  1  0  0  0  0
	  4  9  1  0  0  0  0
	  4 27  1  0  0  0  0
	  5  6  1  0  0  0  0
	  5  7  1  0  0  0  0
	  5 18  1  0  0  0  0
	  5 19  1  0  0  0  0
	  6  8  2  0  0  0  0
	  ......

In addition, if the option to output scores is selected, a tabular file will be created.
Each line represents a molecule from the database, with columns describing the volumes 
of the reference and database molecules, overlap volumes, and Shape-it scores produced 
by the three scoring schemes.

* Example::

	dbName  refName Shape-it::Tanimoto      Shape-it::Tversky_Ref   Shape-it::Tversky_Db    overlap refVolume       dbVolume
	3033    3037    0.562                   0.754                   0.688                   128.56  169.59          187.87


]]>
    </help>
    <citations>
        <citation type="doi">10.1021/j100011a016</citation>
    </citations>
</tool>