<tool id="viennarna_rnacofold" name="@EXECUTABLE@" version="@VERSION@.0">
    <description>Calculate secondary structures of two RNAs with dimerization</description>
    <macros>
        <token name="@EXECUTABLE@">RNAcofold</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        RNAcofold  < '$input' > '$tabularFile'
        -T$model_options.temperature -d$model_options.dangling        
        $general_options.noPS
        $general_options.noconversion        
        $IDs.auto_id
        #if str($IDs.id_prefix) <> "alignment"
            --id-prefix='$IDs.id_prefix'
        #end if
        #if $IDs.id_digits <> 4
            --id-digits=$IDs.id_digits
        #end if
        #if $IDs.id_start <> 1
            --id-start=$IDs.id_start
        #end if        
        #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
            --constraint='$constraints.constraintLocation.constraintsFile'
            $constraints.constraintLocation.canonicalBPonly
            $constraints.constraintLocation.enforceConstraint                
        #end if
        #if str($constraints.constraintLocation.constraintSelector) == "inFile" 
            -C
        #end if
        $algorithm_options.allpf
        #if len($algorithm_options.concfiles) == 1
            #for $i in $algorithm_options.concfiles
                --concfile='$i.concfile'
            #end for
        #end if
        #if $algorithm_options.pf <> "-1"
            --partfunc=$algorithm_options.pf
        #end if
        #if $algorithm_options.pfScale <> 1.07
            --pfScale=$algorithm_options.pfScale
        #end if
        #if $algorithm_options.bppmThreshold <> 1e-5
            --bppmThreshold=$algorithm_options.bppmThreshold
        #end if
        $algorithm_options.gquad		
        $model_options.notetra
        $model_options.nolp
        $model_options.nogu
        $model_options.noclosinggu
        #if $model_options.nsp
            --nsp='$model_options.nsp'
        #end if
        #if $model_options.betaScale <> 1.0
            --betaScale=$model_options.betaScale
        #end if
        
]]>
    </command>
    <inputs>
        <param format="fasta" name="input" type="data" label="Fasta file"/>
        <section name="general_options" title="General Options">
            <param name="noPS" type="boolean" truevalue="" falsevalue="--noPS" checked="true" label="Produce postscript output" help="" argument="--noPS"/>
            <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" argument="--noconv" help="Avoids confusion with DNA sequences"/>
        </section>
        <section name="IDs" title="Naming Conventions">		
                <param name="auto_id" 
                    type="boolean" truevalue="--auto-id" falsevalue="" checked="false" 
                    label="Automatically generate an ID for each alignment." 
                    help="If this flag is active, RNAalifold ignores any IDs retrieved from the input and automatically generates an ID for each alignment." 
                    argument="--auto-id"/>
                <param name="id_prefix" 
                    type="text" value="alignment" 
                    label="Prefix for automatically generated IDs (as used in output file names)" 
                    help="If this parameter is set, each alignment will be prefixed with the provided string. Hence, the output files will obey the following naming scheme: 'prefix_xxxx_ss.ps' (secondary structure plot), 'prefix_xxxx_dp.ps' (dot−plot), 'prefix_xxxx_aln.ps' (annotated alignment), etc. where xxxx is the alignment number beginning with the second alignment in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input alignment." 
                    argument="--id-prefix"/>
                <param name="id_digits" 
                    type="integer" value="4" min="1" max="18" 
                    label="The number of digits of the counter in automatically generated alignment IDs" 
                    help="When alignments IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left−padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]." 
                    argument="--id-digits"/>
                <param name="id_start" 
                    type="integer" value="1" min="0" 
                    label="First number in automatically generated alignment IDs" 
                    help="When alignment IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous alignment IDs, i.e. it activates the −−continuous−ids flag.." 
                    argument="--id-start"/>
        </section>
        <section name="model_options" title="Model Options" expanded="true">
            <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="(-T)"/>
            <param name="dangling" type="select" label="How to treat dangling end energies" help="(-d)">
                <option value="0">0: ignore dangling ends</option>
                <option value="1">1: only unpaired bases can participate in at most one dangling end, this is the default for mfe folding but unsupported for the partition function folding</option>
                <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
                <option value="3">3: mfe folding will allow coaxial stacking of adjacent helices in multi−loops.</option>
            </param>
            <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
            <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
            <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
            <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
            <param name="nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs."
               help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA  will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." 
               argument="--nsp"/>
            <param name="betaScale" type="float" value="1.0" label="Scaling of Boltzman factors" 
                help=" The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types." 
                argument="--betaScale"/>
        </section>
        <section name="constraints" title="Structure constraints">
                <conditional name="constraintLocation">
                    <param name="constraintSelector" type="select" label="Constraints">
                      <!--	<option value="fromInput">The constraints are included in the input file</option> -->
                        <option value="fromFile">The constraints are in a seperate file</option>
                        <option value="inFile">The constraints are in the fasta input file</option>
                        <option value="none" selected="true">Don't use constraints</option>
                    </param>
                    <!-- <when value="fromInput"></when> -->
                    <when value="none"></when>
                    <when value="inFile"></when>
                    <when value="fromFile">
                        <param name="constraintsFile" type="data" format="txt" label="Constraints file" argument="--constraint"/>
                        <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from he structure constraint" />
                        <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
                    </when>
                </conditional>				
        </section>
        <section name="algorithm_options" title="Algorithm Options">
            <param name="pf" type="select" label="Calculate partition function" help="Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only." argument="-p">
                <option value="-1" selected="true">None</option>
                <option value="0">0: Deactivates the calculation of the pair probabilities, saving about 50% in runtime</option>
                <option value="1" >1: Calculate the partition function and base pairing probability matrix</option>				
            </param>
            <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers as well as A and B monomers" help="--all_pf"/>
            <param argument="-c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Concentrations" help="In addition to everything listed under the -a option, read in initial monomer concentrations and compute the expected equilibrium concentrations of the 5 possible species (AB, AA, BB, A, B)."/>
            <repeat name="concfiles" title="A file with initial concentrations for the two sequences" default="0" max="1" help="The table consits of arbitrary many lines with just two numbers (the concentration of sequence A and B). This option will automatically toggle the −c (and thus -a and --all_pf) options">
                <param type="data" name="concfile" format="txt" label="Concentrations file"/>
            </repeat>			
            <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>
            <param argument="--bppmThreshold" type="float" value="1e-5" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data."/>
            <param argument="--gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="take into account G Quadruplex formation"/>
        </section>      
    </inputs>
    <outputs>
        <data format="txt" name="tabularFile"/>
        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
        </collection>
        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
            <filter>pf is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnacofold_input1.fas"/>
            <output name="out_file" file="rnacofold_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
**RNAcofold**


-----

**Input format**

RNAcofold requires one input file:

- Fasta file

Two different RNA sequences can be specified concatenated with the '&' character. The folding of the two sequences with each other will be calculated.


------

**Outputs**

- Energies of the RNA sequences and the dimers
- Structure images
- Dot Plot Matrix images (if --partfunc is used)

]]>
    </help>
    <expand macro="citations" />
</tool>