<tool id="rnasnoop" name="RNAsnoop" version="2.1.6.0">
    <description> Find targets of a query H/ACA snoRNA</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAsnoop</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAsnoop --query=$input1 --target=$input2 > $output
        --alignmentLength=$length
        $constraint
        --energy-threshold=$energyThreshold
        #if $varExists('$advancedOptions.extensioncost')
            $advancedOptions.fast
            --extension-cost=$advancedOptions.extensioncost
            --minimal-right-duplex=$advancedOptions.minrightduplex
            --minimal-loop-energy=$advancedOptions.minloop
            --minimal-left-duplex=$advancedOptions.minleftduplex
            --minimal-duplex=$advancedOptions.minduplex
            --duplex-distance=$advancedOptions.duplexdist
            --minimal-stem-length=$advancedOptions.minstemlength
            --maximal-stem-length=$advancedOptions.maxstemlength
            --minimal-duplex-box-length=$advancedOptions.minbox
            --maximal-duplex-box-length=$advancedOptions.maxbox
            --minimal-snoRNA-stem-loop-length=$advancedOptions.minsnornastem
            --maximal-snoRNA-stem-loop-length=$advancedOptions.maxsnornastem
            --minimal-snoRNA-duplex-length=$advancedOptions.minsnornaduplex
            --maximal-snoRNA-duplex-length=$advancedOptions.maxsnornaduplex
            --minimal-duplex-stem-energy=$advancedOptions.minduplexstem
            --minimal-total-energy=$advancedOptions.mintotal
            --maximal-stem-asymmetry=$advancedOptions.maxstemasymmetry
            --minimal-lower-stem-energy=$advancedOptions.minstemenergy
        #end if
        #if $filetypeOptions.filetypeSelector == "fasta"
            ; tar -cf $imagesFile *.ps
        #else
            --alignment-mode
        #end if
]]>
    </command>

    <inputs>
        <conditional name="filetypeOptions">
            <param name="filetypeSelector" type="select" label="Select Filetype">
                <option value="fasta" selected="true">Fasta</option>
                <option value="clustal">Clustal</option>
            </param>
            <when value="fasta">
                <param format="fasta" name="input1" type="data" label="Query sequences"/>
                <param format="fasta" name="input2" type="data" label="Target sequences"/>
            </when>
            <when value="clustal">
                <param format="txt" name="input1" type="data" label="Query sequences"/>
                <param format="txt" name="input2" type="data" label="Target sequences"/>
            </when>
        </conditional>


        <param name="length" type="integer" min="0" value="25" label="Maximal alignment length" help="--alignmentLength"/>
        <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate the stem structure subject to constraints" help="--constraint"/>
        <param name="energyThreshold" size="8" type="float" value="-1.0" label="Maximal energy difference between the mfe and the desired suboptimal structure" help="--energy-threshold"/>

        <conditional name="advancedOptions">
            <param name="advancedSelector" type="select" label="advanced options">
                <option value="basic">basic Options</option>
                <option value="advanced">advanced Options</option>
            </param>
            <when value="advanced">
                <param name="fast" type="boolean" truevalue="--fast-folding=1" falsevalue="--fast-folding=0" checked="true" label="Backtracking based on the standard energy model" help="--fast-folding"/>
                <param name="extensioncost" type="integer" value="0" label="Cost to add each nucleotide in a duplex" help="--extension-cost"/>
                <param name="minrightduplex" type="integer" value="-270" label="Minimal right duplex energy" help="--minimal-right-duplex"/>
                <param name="minloop" type="integer" value="-280" label="Minimal Loop energy" help="--minimal-loop-energy"/>
                <param name="minleftduplex" type="integer" value="-170" label="Minimal left duplex energy" help="--minimal-left-duplex"/>
                <param name="minduplex" type="integer" value="-1090" label="Minimal duplex energy" help="--minimal-duplex"/>
                <param name="duplexdist" type="integer" value="2" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/>
                <param name="minstemlength" type="integer" value="5" label="Minimal snoRNA stem length" help="--minimal-stem-length"/>
                <param name="maxstemlength" type="integer" value="120" label="Maximal snoRNA stem length" help="--maximal-stem-length"/>
                <param name="minbox" type="integer" value="11" label="Minimal distance between the duplex end and the H/ACA box" help="--minimal-duplex-box-length"/>
                <param name="maxbox" type="integer" value="16" label="Maximal distance between the duplex end and the H/ACA box" help="--maximal-duplex-box-length"/>
                <param name="minsnornastem" type="integer" value="1" label="Minimal distance between the stem loop and the snoRNA sequence" help="--minimal-snoRNA-stem-loop-length"/>
                <param name="maxsnornastem" type="integer" value="100000" label="Maximal distance between the stem loop and the snoRNA sequence" help="--maximal-snoRNA-stem-loop-length"/>
                <param name="minsnornaduplex" type="integer" value="0" label="Minimal distance between the duplex and the snoRNA sequence" help="--minimal-snoRNA-duplex-length"/>
                <param name="maxsnornaduplex" type="integer" value="0" label="Maximal distance between the duplex and the snoRNA sequence" help="--maximal-snoRNA-duplex-length"/>
                <param name="minduplexstem" type="integer" value="-1370" label="Minimal duplex stem energy" help="--minimal-duplex-stem-energy"/>
                <param name="mintotal" type="integer" value="100000" label="Minimal total energy" help="--minimal-total-energy"/>
                <param name="maxstemasymmetry" type="integer" value="30" label="Maximal snoRNA stem asymmetry" help="--maximal-stem-asymmetry"/>
                <param name="minstemenergy" type="integer" value="100000" label="Minimal lower stem energy" help="--minimal-lower-stem-energy"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="output"/>
        <data format="tar" name="imagesFile">
             <filter>filetypeOptions['filetypeSelector'] == "fasta"</filter>
        </data>

    </outputs>
    <tests>
        <test>
            <param name="input1" value="rnasnoop_input1b.fa"/>
            <param name="input2" value="rnasnoop_input1a.fa"/>
            <output name="output" file="rnasnoop_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

**RNAsnoop**

reads a target RNA sequence and a H/ACA snoRNA sequence from a target and query file, respectively and computes optimal and suboptimal secondary structures for their hybridization. The calculation can be done roughly done in O(nm), where is n the length of the target sequence and m is the length of the snoRNA stem, as it is specially tailored to the special case of H/ACA snoRNA. For general purpose target predictions, please have a look at RNAduplex, RNAup, RNAcofold and RNAplex.


-----

**Input format**

RNAsnoop requires two input files

- either two Fasta files
- or two Clustal alignment files

------

**Outputs**

The computed optimal and suboptimal structure are given, one structure per line. Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The '<>' brackets represent snoRNA intramolecular interactions, while the '()' brackets represent intermolecular interactions between the snoRNA and its target.
The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. If available the opening energy are also returned.


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