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<tool id="rbc_kinwalker" name="Kinwalker" version="1.0">
    <description>
<![CDATA[
cotranscriptional folding of RNAs
]]>
    </description>
    <requirements>
        <requirement type="package" version="1.0">kinwalker</requirement>
        <requirement type="package" version="8.22">gnu_coreutils</requirement>
        <requirement type="package" version="2.1">vienna_rna</requirement>
    </requirements>
    <command>
<![CDATA[
    head -n 1 $input_sequence | head -c -1 -q  > seq.ident
    &&
    sed '1d' $input_sequence > input.seq
    &&
    kinwalker
        $init_structure
        $interrupt
        ##$printfront
        
        --barrier_heuristic $barrier_heuristic.used
        
        #if $barrier_heuristic.used == "M"
            --grouping $barrier_heuristic.grouping
            --lookahead $barrier_heuristic.lookahead
        #else if $barrier_heuristic.used == "B"
            --maxkeep $barrier_heuristic.maxkeep
        #end if
        
        --dangle $dangle
        --noLonelyPairs $noLonelyPairs
        --transcribed $transcribed
        --transcription_rate $transcription_rate
        --windowsize $windowsize
        
        < input.seq
        
        > blah
         
        &&
        sed -n '2s/[\.\(\)]\+\s\+\(.\+\)$/ mfe: \1/p' blah > energy
        
        &&
        cat seq.ident energy > $mfe_struct
        
        &&
        sed -e '2s/^\([\.\(\)]\+\).*$/\1/' -ne '1,2p' blah >> $mfe_struct
        
        &&
        sed -e 's/[ \t]*$//' -ne '/TRAJ/,/Kinwal/ {/TRAJ/n;/Kinwal/!{s/\s/\t/gp}}' blah > $trajectory
]]>
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <inputs>
        <param name="input_sequence" format="fasta" type="data" label="Input sequence" help="A single sequence in FASTA format"/>
        <param name="init_structure" type="boolean" truevalue="--init_structure" falsevalue="" checked="false" label="Start with a structure other than the open chain" help="(--init_structure)"/>
        <param name="interrupt" type="boolean" truevalue="--interrupt" falsevalue="" checked="false" label="Allow interrupted folding trajectories when the barrier is exceeded" help="(--interrupt)"/>
        <!-- need to implement with dataset collections <param name="printfront" type="boolean" truevalue="!doublehypen!printfront" falsevalue="" checked="true" label="Creates PS plots of front progression" help="(!doublehypen!printfront)"/> -->
        <conditional name="barrier_heuristic">
            <param name="used" type="select" label="Barrier Heuristic" help="(--barrier_heuristic)">
                <option value="M" selected="true">Morgan-Higgs</option>
                <option value="S">Limit small stacks</option>
                <option value="B">Barriers</option>
                <option value="A">All</option>
            </param>
            <when value="M">
                <param name="grouping" type="select" label="How to treat conflict groups" help="(--grouping)">
                    <option value="standard" selected="true">Standard</option>
                    <option value="regroup">Re-group</option>
                </param>
                <param name="lookahead" type="integer" value="1" label="Number of basepairs that MorganHiggs forms its subpaths from" help="(--lookahead)"/>
            </when>
            <when value="S" />
            <when value="B">
                <param name="maxkeep" type="integer" value="1" label="Breadth of breadth first search" help="(--maxkeep)"/>
            </when>
            <when value="A" />
        </conditional>
        <param name="dangle" type="select" label="Dangle value as in VienneRNA package" help="(--dangle)">
            <option value="0" selected="true">0</option>
            <option value="1">1</option>
            <option value="2">2</option>
        </param>
        <param name="noLonelyPairs" type="integer" value="2" label="Value of noLonelyPairs as in ViennaRNA" help="(--noLonelyPairs)"/>
        
        <param name="transcribed" type="integer" value="1" label="Number of bases initially transcribed" help="0 means all is transcribed (--transcribed)"/>
        <param name="transcription_rate" type="float" value="200" label="Number of bases transcribed per second" help="(--transcription_rate)"/>
        <param name="windowsize" type="integer" value="0" label="Max size of substructures considered for folding events during transcription" help="0= all are considered. (--windowsize)"/>
    </inputs>
    <outputs>
        <data format="fasta" name="mfe_struct" label="MFE structure from ${tool.name} on ${on_string}" />
        <data format="tabular" name="trajectory" label="Trajectory of ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input_sequence" value="test_sequence.fasta" />
            <param name="init_structure" value="" />
            <param name="interrupt" value="" />
            <param name="used" value="M" />
            <param name="grouping" value="standard" />
            <param name="lookahead" value="1" />
            <param name="dangle" value="0" />
            <param name="noLonelyPairs" value="2" />
            <param name="transcribed" value="1" />
            <param name="transcription_rate" value="200" />
            <param name="windowsize" value="0" />
            <output name="mfe_struct" file="mfe_struct.fasta" />
            <output name="trajectory" file="trajectory.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
**What Kinwalker does**

Kinwalker splits the folding process into a series of events where each event can either be a folding event or  a  transcription event.   
In  each  transcription  event one base from the RNA sequence is appended to the already transcribed and (partially) folded subsequence. 
Kinwalker executes transcription events at regular time intervals. In each folding event a subsequence  of  the  already  transcribed 
RNA sequence is selected and a new structure is formed by combining base pairs from the current structure with base pairs from the 
mfE structure of that subsequence. 

This is done in such a way that the new  structure  includes  base  pairs from both structures in an energetically favorable manner. 
Kinwalker estimates the waiting times for individual folding events depending on the height of the energy barrier between the 
current structure and the new  structure  into which the molecule is folded. Folding events between structures can only occur, 
if the energy barrier between them is less than the maximum allowed energy barrier. 

As folding paths can only be calculated  exhaustively  for  short  sequences (n>100),  heuristic  approaches have to be employed which explicitly 
construct a (re)folding path between the two structures. The saddle height is then estimated as the highest point along the path. 
The best known algorithm  for  approximating  saddle heights  between RNA conformations is the Morgan-Higgs heuristic, 
which tries to find a folding path from an origin secondary structure to a target secondary structure where the maximum height 
along the path is  minimal.  The  heuristic  models  state transitions at base pair resolution.
]]>
    </help>
    <citations>
        <citation type="doi">10.1016/j.jmb.2008.02.064</citation>
    </citations>
</tool>