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<tool id="acpc" name="ACPC" version="1.0">
    <description>Chemoinformatics tool for ligand-based virtual screening</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[ 
        #if $program_chose.program=="acpc" #
            if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then 
                cat $program_chose.q > query.mol2;
                cat $program_chose.db > database.mol2 ;
            else
                if cat $program_chose.q | grep "BEGIN" > /dev/null; then 
                    cat $program_chose.q > query.pl;
                    cat $program_chose.db > database.pl ;
                else
                    cat $program_chose.q > query.pqr;
                    cat $program_chose.db > database.pqr ;
                fi;
            fi;
            acpc 
                -q query.*
                -db database.*
                #if $program_chose.top_mol.top_scoring_mol=="true"
                -top $program_chose.top_mol.top
                -o mol_output
                #end if
                #if $program_chose.a
                -a $program_chose.a
                #end if
                #if $program_chose.nopp=="true"
                -nopp
                #end if
                #if $program_chose.er
                -er $program_chose.er
                #end if
                #if $program_chose.scan=="true"
                -scan scan_out
                #end if
                -v
                ;
            cat *.scores > $score_output_acpc;
            #if $program_chose.top_mol.top_scoring_mol=="true" #
                cat mol_output > $mol_output_acpc;
            #end if #
            #if $program_chose.scan=="true" #
                cat scan_out > $scan_output_acpc;
                cat query.mol2.bld > $bld_output_acpc;
            #end if #
        #end if #
        #if $program_chose.program=="acpc_mol2tool" #
            cat $program_chose.i > query.mol2;
            acpc_mol2tool -i query.mol2;
            mkdir results;
            mv query_*/* results/. ;
        #end if #
        #if $program_chose.program=="acpc_par" #
            if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then 
                cat $program_chose.q > query.mol2;
                cat $program_chose.db > database.mol2 ;
            else
                if cat $program_chose.q | grep "BEGIN" > /dev/null; then 
                    cat $program_chose.q > query.pl;
                    cat $program_chose.db > database.pl ;
                else
                    cat $program_chose.q > query.pqr;
                    cat $program_chose.db > database.pqr ;
                fi;
            fi;
            acpc_par 
                -q query.*
                -db database.*
                -o score
                #if $program_chose.a
                -a $a
                #end if
                #if $program_chose.np
                -np $np
                #end if
                ;
            cat score > $output_acpc_par;
        #end if #
        #if $program_chose.program=="acpc_pqrtool" #
            cat $program_chose.pqrfile > pqrfile.pqr;
            acpc_pqrtool pqrfile.pqr > $output_acpc_pqrtool;
        #end if #  
        #if $program_chose.program=="acpc_mol2reader" #
            cat $program_chose.mol2file > mol2file.mol2;
            acpc_mol2reader mol2file.mol2 > $output_acpc_mol2reader;
        #end if #        
        #if $program_chose.program=="acpc_auctool" #
            cat $program_chose.i > score.scores;
            acpc_auctool -i score.scores -p $program_chose.p > $output_acpc_auctool;
        #end if #
        #if $program_chose.program=="acpc_pltool" #
            cat $program_chose.plfile > plfile.pl;
            acpc_pltool plfile.pl > $output_acpc_pltool;
        #end if #

        ]]>
    </command>
    <inputs>
        <conditional name="program_chose">
            <param name="program" type="select" label="Chose a program ">
                <option value="acpc" selected="true">acpc </option>
                <!-- <option value="acpc_consrank">acpc_consrank </option> -->
                <option value="acpc_mol2tool">acpc_mol2tool </option>
                <option value="acpc_pqrtool">acpc_pqrtool </option>
                <option value="acpc_auctool">acpc_auctool </option>
                <!-- <option value="acpc_ertool">acpc_ertool </option> -->
                <option value="acpc_par">acpc_par </option>
                <!-- <option value="acpc_scorer">acpc_scorer </option> -->
                <!-- <option value="acpc_codec">acpc_codec </option> -->
                <option value="acpc_mol2reader">acpc_mol2reader </option>
                <option value="acpc_pltool">acpc_pltool </option>
            </param>
            <when value="acpc">
                <param name="q" type="data" format="mol2,pqr,pl" label="Query" help="acpc (-q)" />
                <param name="db" type="data" format="mol2,pqr,pl" label="Database" help="acpc (-db)" />
                <param name="a" type="float" label="Kernel parameter (default depends on considered feature space and was optimized on DUD-E)" help="acpc (-a)" optional="true" />
                <param name="er" type="float" label="Enrichment rate parameter; e.g. 0.01 --> ER_1%" help="acpc (-er)" optional="true">
                    <validator type="in_range" min="0" max="1" />
                </param>
                <param name="nopp" type="select" label="Don't rm duplicate molecules (based on names)" help="acpc (-nopp)">
                    <option value="false" selected="true">Don't use this option</option>
                    <option value="true">Use this option</option>
                </param>
                <param name="scan" type="select" label="Scan delta AUC per atom in the query and create a new query molecule" help="acpc (-scan)">
                    <option value="false" selected="true">Don't use this option</option>
                    <option value="true">Use this option</option>
                </param> 
                <conditional name="top_mol" >
                    <param name="top_scoring_mol" type="select" label="Return file with top scoring molecules (only works for MOL2 files)" >
                        <option value="false" selected="true">Don't use this option</option>
                        <option value="true">Use this option</option>
                    </param>
                    <when value="false" >
                    </when>
                    <when value="true" >
                        <param name="top" type="integer" value="1" label="Number of top scoring molecules to output" help="acpc (-top)" />
                    </when>
                </conditional>               
            </when>
            <!-- <when value="acpc_consrank"> -->
            <!-- </when> -->
            <when value="acpc_mol2tool">
                <param name="i" type="data" format="mol2" label="Input mol2 file" help="acpc_mol2tool (-i)" />
            </when>
            <when value="acpc_pqrtool">
                <param name="pqrfile" type="data" format="pqr" label="Input pqr file" /> 
            </when>
            <when value="acpc_auctool">
                <param name="i" type="data" format="data" label="Input score file" />
                <param name="p" type="text" value="0.05" label="A float such that x in (0.0; 1.0] " />
            </when>
            <!-- <when value="acpc_ertool"> -->
            <!-- </when> -->
            <when value="acpc_par">
                <param name="q" type="data" format="mol2" label="Query" help="acpc_par (-q)" />
                <param name="db" type="data" format="mol2" label="Database" help="acpc_par (-db)" />
                <param name="a" type="float" label="Kernel parameter (default depends on considered feature space and was optimized on DUD-E)" help="acpc_par (-a)" optional="true" />
                <param name="np" type="integer" label="Max number of cores to use" help="acpc_par (-np)" optional="true" />
            </when>
            <!-- <when value="acpc_scorer"> -->
            <!-- </when> -->
            <!-- <when value="acpc_codec"> -->
            <!-- </when> -->
            <when value="acpc_mol2reader">
                <param name="mol2file" type="data" format="mol2" label="Input mol2 file" /> 
            </when>
            <when value="acpc_pltool">
                <param name="plfile" type="data" format="pl" label="Input pl file" /> 
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="mol_output_acpc" format="txt" label="ACPC: output molecules" >
            <filter>program_chose["program"]=="acpc" and program_chose["top_mol"]["top_scoring_mol"]=="true"</filter>
        </data>        
        <data name="score_output_acpc" format="txt" label="ACPC: score" >
            <filter>program_chose["program"]=="acpc"</filter>
        </data>
        <data name="scan_output_acpc" format="txt" label="ACPC: scan file">
            <filter>program_chose["program"]=="acpc" and program_chose["scan"]=="true"</filter>
        </data>        
        <data name="bld_output_acpc" format="txt" label="ACPC: mol2.bld file">
            <filter>program_chose["program"]=="acpc"</filter>
            <filter>program_chose["scan"]=="true"</filter>
        </data>
        <data format="txt" name="report">
            <filter>program_chose["program"]=="acpc_mol2tool"</filter>
            <discover_datasets pattern="([0123456789]*)\.mol2" directory="results" visible="true" />
        </data>
        <data name="output_acpc_par" format="txt" label="ACPC: score file">
            <filter>program_chose["program"]=="acpc_par" </filter>
        </data>         
        <data name="output_acpc_mol2reader" format="txt" label="ACPC mol2reader output">
            <filter>program_chose["program"]=="acpc_mol2reader" </filter>
        </data>         
        <data name="output_acpc_pltool" format="txt" label="ACPC pltool output">
            <filter>program_chose["program"]=="acpc_pltool" </filter>
        </data>         
        <data name="output_acpc_auctool" format="txt" label="ACPC auctool output">
            <filter>program_chose["program"]=="acpc_auctool" </filter>
        </data>         
        <data name="output_acpc_pqrtool" format="txt" label="ACPC pqrtool output">
            <filter>program_chose["program"]=="acpc_pqrtool" </filter>
        </data> 
    </outputs>
    <tests>
        <test>
            <param name="program" value="acpc" />
            <param name="top_scoring_mol" value="true" />
            <param name="q" value="acpc/query.mol2" />
            <param name="db" value="acpc/database.mol2" />
            <output name="mol_output_acpc" file="acpc/output"/>
        </test>        
        <test>
            <param name="program" value="acpc_mol2reader" />
            <param name="mol2file" value="acpc/query.mol2" />
            <output name="output_acpc_mol2reader" file="acpc/output_mol2reader"/>
        </test>
    </tests>
    <help>
        <![CDATA[
************
Description
************
ACPC is a ligand-based virtual screening tool using AutoCorrelation of Partial Charges. 

*******
Help
*******
    
    acpc 
    
      --a float                   kernel parameter (default depends on considered feature space and was optimized on DUD-E)
      --db db                     database in .mol2, .pl or .pqr format
      --er x                      enrichment rate parameter; e.g. 0.01 --> ER_1%
      --nopp                      don't rm duplicate molecules (based on names)
      --q query                   query in .mol2, .pl or .pqr format
      --scan out_file             scan delta AUC per atom in the query and create a new query molecule
      --top int                   number of top scoring molecules to output (only works for MOL2 files)
    
    
    acpc_mol2tool
    
      --i in   input mol2 file
    
    acpc_auctool
    
      -i in        input scores file
      -p x         a float such that 0.0 < x <= 1.0 
    
    
    
    acpc_par
    
      --a float                   kernel parameter (default was optimized on DUD-E and depends on considered feature space)
      --db db                     molecules database in .mol2, .pl or .pqr format
      --q                         query molecule in .mol2, .pl or .pqr format
      --np int                    max number of cores to use
    
        ]]>
    </help>
    <citations>
        <citation type="bibtex">
            @article{Berenger2014,
              doi = {10.1186/1758-2946-6-23},
              url = {http://dx.doi.org/10.1186/1758-2946-6-23},
              year  = {2014},
              publisher = {Springer Nature},
              volume = {6},
              number = {1},
              pages = {23},
              author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
              title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
              journal = {Journal of Cheminformatics}
            }
        </citation>
    </citations>
</tool>