annotate rnafold.xml @ 1:ec0fdb8c4ebb draft

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<tool id="rnafold" name="RNAfold" version="2.1.6.0">
    <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAfold</token>
        <import>macros.xml</import>
    </macros>
    <command>
 <![CDATA[
    RNAfold
    -T $temperature
    --dangles=$dangling
    #if $measelect.mea == "yes":
        --MEA=$measelect.meavalue
    #else
        $measelect.pf
    #end if
    #if $varExists('$advancedOptions.nogu'):
        $advancedOptions.noconversion
        $advancedOptions.gquad
        $advancedOptions.nolp
        $advancedOptions.nogu
        $advancedOptions.noclosinggu
        $advancedOptions.canonicalonly
        $advancedOptions.circular
    #end if

    < $fasta_input

    > $tabular_file
]]>
    </command>

    <inputs>
    <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
        <param name="temperature" size="6" 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: 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>
        <conditional name="measelect">
            <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
            </when>
            <when value="no">
                <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
            </when>
        </conditional>
        <conditional name="advancedOptions">
            <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/>
            <when value="true">
                <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
                <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
                <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP  don't allow lonely pairs."/>
                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU  don't allow pairing of G and U at the ends of helices."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
                <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
                <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="tabular_file"/>
        <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>measelect['pf'] is True</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
        </collection>
          
    </outputs>
    <tests>
    </tests>
    <help>
<![CDATA[
**RNAfold**

The program reads RNA sequences, calculates their minimum free
energy (mfe) structure and the mfe structure in dot-bracket notation.

If the -p option was given it also computes the
partition function (pf) and base pairing probability matrix.

The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
probability in the upper right half, and one square for each pair in the
minimum free energy structure in the lower left half. For each pair i-j with
probability p>10E-6 there is a line of the form

i  j  sqrt(p)  ubox

in the PostScript file, so that the pair probabilities can be easily extracted.

The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively.
The program will read the whole FASTA input file and provide output for each found sequence.


-----

**Input format**

RNAfold requires one input file
- FASTA file

------

**Outputs**

- Secondary structures in dot-bracket notation

- several possible postscript images bundled together in a tar file
    - secondary structure for each sequence in the input file
    - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence 

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