annotate rnaaliduplex.xml @ 0:d4f6c7ba5f69 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9

<tool id="viennarna_rnaaliduplex" name="@EXECUTABLE@" version="@VERSION@.0">
    <description>find binding sites of two RNA alignments</description>
    <macros>
        <token name="@EXECUTABLE@">RNAaliduplex</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        RNAaliduplex -T $temperature -d $dangling $flagsort --deltaEnergy=$deltaEnergy '$input1' '$input2'
        $advancedOptions.noconversion
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.notetra
        #if $advancedOptions.nsp
            --nsp='$advancedOptions.nsp'
        #end if
        > '$out_file'
]]>
    </command>
    <inputs>
        <param format="txt" name="input1" type="data" label="Clustal alignment file"/>
        <param format="txt" name="input2" type="data" label="Clustal alignment file"/>
        <param name="temperature" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
        <param argument="--deltaEnergy" type="float" value="0.0" label="Compute suboptimal structures with energy in a certain range of the optimum [kcal/mol]" 
            help="Default is calculation of mfe structure only."/>
        <param name="dangling" type="select" label="How to treat dangling end energiesHow to treat dangling end energies for bases adjacent to helices in free ends and multi-loops" argument="-d">
            <option value="0">0: ignore dangling ends</option>
            <option value="1">1: unpaired bases participate in one dangling end only</option>
            <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
            <option value="3">3: allow coaxial stacking</option>
        </param>
        <param name="flagsort" type="boolean" checked="false" label="Output will be sorted by free energy" truevalue="--sorted" falsevalue="" help="--sorted"/>
        <section name="advancedOptions" title="Advanced options">
            <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="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>
            <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"/>
        </section>
    </inputs>
    <outputs>
        <data format="dbn" name="out_file"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="rnaaliduplex_input1.clustal"/>
            <param name="input2" value="rnaaliduplex_input1.clustal"/>
            <output name="out_file1" file="rnaaliduplex_result1.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
**RNAaliduplex**

The program reads two alignments of RNA sequences in CLUSTAL format and
predicts optimal and suboptimal binding sites, hybridization energies and the
corresponding structures. The calculation takes only inter-molecular base pairs
into account, for the general case use RNAcofold. The use of alignments allows
to focus on binding sites that are evolutionary conserved. Note, that the two
input alignments need to have an equal number of sequences and the same order,
i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc.

The computed binding sites, energies, and structures are written to stdout, one
structure per line. Each line consist of: The structure in dot bracket format
with a &  separating the two strands. The range of the structure in the two
sequences in the format  "from,to : from,to"; the energy of duplex structure
in kcal/mol.
The format is especially useful for computing the hybrid structure between a
small probe sequence and a long target sequence.



-----

**Input format**

RNAaliduplex takes two alignment files generated with Clustal (\*.aln).


-----

**Outputs**

text output with several secondary structures and its energies

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