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<tool id="lisica" name="LiSiCA" version="1.0">
    <description>A Software for Ligand-Based Virtual Screening</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[ 
        $__tool_directory__/tools/lisica/lisica 
                                                -R $R
                                                -T $T
                                                #if $n
                                                -n $n
                                                #end if
                                                -d $graph_dimension.d
                                                #if $graph_dimension.d=="2"
                                                -s $graph_dimension.s
                                                #end if
                                                #if $graph_dimension.d=="3"
                                                -m $graph_dimension.m
                                                #end if
                                                #if $h=="true"
                                                -h
                                                #end if
                                                > $output;

        ]]>
    </command>
    <inputs>
        <param name="R" type="data" format="mol2" label="Reference molecule" help="(-R)" />
        <param name="T" type="data" format="mol2" label="Target molecules" help="(-T)" />
        <param name="n" type="integer" label="The number of CPUs to use" help="(-n)" optional="true" />
        <conditional name="graph_dimension">
            <param name="d" type="select" label="Product graph dimension" help="(-d)" >
                <option value="2" selected="true">2</option>
                <option value="3">3</option>
            </param>
            <when value="2">
                <param name="s" type="float" value="1" label="Maximum allowed shortest path size for 2D product graph" help="(-s)" />
            </when>            
            <when value="3">
                <param name="m" type="float" value="1" label="Maximum allowed atom spatial distance for 3D product graph" help="(-m)" />
            </when>
        </conditional>
        <!-- <param name="w" type="integer" label="number of highest ranked molecules to write to output" optional="true" help="(-w)" /> -->
        <param name="h" type="select" label="Consider hydrogens" help="(-h)" >
            <option value="true" >
                Use this option
            </option>
            <option value="false" selected="true" >
                Do not use this option
            </option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="R" value="lisica/reference.mol2" />
            <param name="T" value="lisica/database.mol2" />
            <output name="output" file="lisica/output.txt" />
        </test>
    </tests>
    <help>
        <![CDATA[
***********
Description
***********
LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly.

******
Help
******
    Use: ./lisica -R <reference molecule> -T <target molecules> [parameters]

    **Parameters**
    
    -n  the number of CPUs to use  
    -d  product graph dimension, possible input: 2, 3 
    -m  maximum allowed atom spatial distance for 3D product graph
    -s  maximum allowed shortest path size for 2D product graph
    -h  consider hydrogens
        ]]>
    </help>
    <citations>
        <citation type="bibtex">
            @article{lešnik2015lisica,
             title={LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors},
             author={Lešnik, Samo and Štular, Tanja and Brus, Boris and Knez, Damijan and Gobec, Stanislav and Janežič, Dušanka and Konc, Janez},
             journal={Journal of chemical information and modeling},
             volume={55},
             number={8},
             pages={1521--1528},
             year={2015},
             publisher={ACS Publications}
            }
        </citation>
    </citations>
</tool>