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<tool id="cofold" name="Cofold" version="0.0.1">
    <description>An RNA secondary structure prediction method that takes co-transcriptional folding into account</description>
    <requirements>
        <requirement type="package" version="0.0.1"></requirement>
    </requirements>
    <version_command>CoFold --version</version_command>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command interpreter="python">
<![CDATA[
        cofold.py
            -i $infile
            -o1 $tabularFile
            --parameters " -T$temperature -d$dangling
                -P $energy_parameter
                --distAlpha $distAlpha
                --distTau $distTau
                #if $advancedOptions.advancedSelector == 'yes':
                    $advancedOptions.constraint
                    $advancedOptions.noconversion
                    $advancedOptions.nolp
                    $advancedOptions.nogu
                    $advancedOptions.noclosinggu
                    $advancedOptions.notetra
                    $advancedOptions.circular
                #end if
            ";
        count=`ls -l *.ps | wc -l`;
        echo '#RNA structures: '\$count > $report;
]]>
    </command>
    <inputs>
        <param format="fasta" name="infile" type="data" label="FASTA file"/>
        <param name="distAlpha" type="float" value="0.5" label="temperature [°C]" help="(--distAlpha)"/>
        <param name="distTau" type="float" value="640.0" label="temperature [°C]" help="(--distTau)"/>
        <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="(-T)"/>
        <param name="energy_parameter" type="select" label="Thermodynamic energy parameters" help="(-P)">
            <option value="rna_turner1999.par" selected="True">Turner 1999</option>
            <option value="rna_turner2004.par">Turner 2004</option>
            <option value="rna_andronescu2007.par">Andronescu 2007</option>
        </param>
        <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="advancedOptions">
            <param name="advancedSelector" type="select" label="Advanced Options">
                <option value="no">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false"
                    label="Calculate structures subject to constraints" help="(--constraint)"/>
                <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false"
                    label="No conversion" help="Do not convert thymine to uracile (T -> U). (--noconv)"/>
                <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false"
                    label="No lonely pairs" help="--noLP  don't allow lonely pairs. (--noLP)"/>
                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false"
                    label="No GU pairing" help="Don't allow pairing of G and U. (--noGU)"/>
                <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false"
                    label="No GU pairing at the ends" help="Don't allow pairing of G and U at the ends of helices. (--noClosingGU)"/>
                <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false"
                    label="No stabilization for loops, hairpins etc." help="(--noTetra)"/>
                <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false"
                    label="Assume circular RNA structure" help="(--circ)"/>
                <param name="noPS" type="boolean" truevalue="--noPS" falsevalue="" checked="false"
                    label="Don't generate PS files" help="(--noPS)"/>
            </when>
            <when value="no" />
        </conditional>
    </inputs>
    <outputs>
        <data name="tabularFile" format="tabular" label="Tabular File"/>
        <data name="report" format="txt" label="RNA PS File" hidden="true">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="rna_eps" visible="true"/>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="cofold1.fasta" ftype="fasta"/>
            <param name="noPS" value="--noPS"/>
            <output name="tabularFile" file="colfold_results1.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="infile" value="cofold1.fasta" ftype="fasta"/>
            <param name="noPS" value="--noPS"/>
            <param name="energy_parameter" value="rna_andronescu2007.par"/>
            <param name="dangling" value="1"/>
            <param name="advancedSelector" value="yes"/>
            <output name="tabularFile" file="colfold_results2.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="infile" value="cofold1.fasta" ftype="fasta"/>
            <param name="noPS" value=""/>
            <output name="tabularFile" file="colfold_results3.tabular" ftype="tabular" />
            <output name="report">
                <assert_contents>
                    <has_line_matching expression="#RNA structures.*" />
                </assert_contents>
                <discovered_dataset designation="example1_ss" file="example1_ss.ps" compare="sim_size" delta="100" ftype="rna_eps"/>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**CoFold**

A tool for prediction of RNA secondary structure that takes co-transcriptional folding into account 

**Input format**

CoFold requires one input file in FASTA format.

------

**Outputs**

- Tab-seperated file
    - 1st column: header line of FASTA input
    - 2nd column: sequence
    - 3rd column: dot-bracket notation
    - 4th column: free energy

]]>
    </help>
    <citations>
        <citation type="doi">doi:10.1093/nar/gkt174</citation>
        <citation type="doi">doi:10.1093/nar/gks241</citation>
    </citations>
</tool>