<tool id="remurna" name="remuRNA" version="1.0.0">
    <description>Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation</description>
    <requirements>
        <requirement type="package" version="1.0">remurna</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
    touch input.fa &&
    python $__tool_directory__/create_input_file.py '$seq' '$snp' input.fa &&
    \$(which remuRNA)
            --proc="\${GALAXY_SLOTS}" ## number of CPUs
            --window=$window
            #if $advanced.advanced_selector =="advanced"
                --NA=$advanced.NA
                #if $advanced.energy == "abs_sig"
                    --energy='|sig|'
                #else
                    --energy='sig'
                #end if
                --tmin=$advanced.tmin
                --tinc=$advanced.tinc
                --tmax=$advanced.tmax
                #if $advanced.suffix
                    --suffix='$advanced.suffix'
                #end if
                --log=$advanced.log
                #if $advanced.sodium
                    --sodium=$advanced.sodium
                #end if
                #if $advanced.magnesium
                    --magnesium=$advanced.magnesium
                #end if
                $advanced.polymer
                $advanced.zip
                $advanced.mutations
                $advanced.nodangle
            #end if
            input.fa
        > '$outfile'
    ]]></command>
    <inputs>
        <param argument="--seq" type="data" format="fasta" label="Input Alignment File" />
        <param argument="--snp" type="data" format="txt"  label="SNP"  help="remuRNA accepts only a single tag in each call."/>
        <param argument="--window" type="integer"  value="200" min="1" label="Windows size" help="Compute average distance over windows of size winsize."/>

        <conditional name="advanced">
            <param name="advanced_selector" type="select" label="Advanced Options">
                <option value="basic">Basic options</option>
                <option value="advanced">Advanced options</option>
            </param>
            <when value="basic"></when>
            <when value="advanced">
                <param argument="--NA" type="select" label="RNA or DNA">
                    <option value="RNA" selected="true">RNA sequence</option>
                    <option value="DNA">DNA sequence</option>
                </param>
                <param argument="--energy" type="select" label="Energy">
                    <option value="abs_sig" selected="true">|sig|</option>
                    <option value="sig">sig</option>
                </param>

                <param argument="--tmin" type="float" value="37.0" label="Min temperature [°C]" help=""/>
                <param argument="--tmax" type="float" value="37.0" label="Max temperature [°C]" help=""/>
                <param argument="--tinc" type="float" value="1.0" label="Temperature increment [°C]" help=""/>

                <param argument="--suffix" type="text" optional="true" label="Suffix" />


                <param argument="--sodium" type="float" optional="true" label="Salt concentration" help=""/>
                <param argument="--magnesium" type="float" optional="true" label="Magnesium concentration" help=""/>
                <param argument="--mutations" type="boolean" truevalue="--mutations" falsevalue="" checked="false"  label="Compute relative entropy for all ppossible point mutations" help=""/>
                <param argument="--nodangle" type="boolean" truevalue="" falsevalue="--nodangle" checked="true"  label="Include dangling energies" help="default, dangling energies will be added for the bases adjacent to a helix on both sides in any case"/>
                <param argument="--polymer" type="boolean" truevalue="--polymer" falsevalue="" checked="false"  label="Polymer" help=""/>
                <param argument="--zip" type="boolean" truevalue="--zip" falsevalue="" checked="false"  label="Zip" help=""/>
                <param argument="--log" type="select" label="Log level">
                    <option value="0">0: OFF</option>
                    <option value="1" selected="true">1: Errors</option>
                    <option value="2">2: Warnings</option>
                    <option value="3">3: Info</option>
                    <option value="4">4: Debug</option>
                    <option value="5">5: All</option>
                </param>
            </when>
        </conditional>

    </inputs>

    <outputs>
         <data name="outfile" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="seq" value="seq.fa"/>
            <param name="snp" value="snp.txt"/>
            <output name="outfile" file="output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

 Measurement of Single-Nucleotide Polymorphism-induced Changes of RNA Conformation

Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanation necessitating the development of methods to measure the impact of single-nucleotide variation on RNA structure. To answer this need, remuRNA commutes the relative entropy between the Boltzmann ensembles of the native and a mutant structure.

**Input**

1.  Sequence file: must contain one sequence in Fasta format.

2.  SNP file: must contain only one tag


**Output**.

SNP	MFE(wt)	MFE(mu)	dMFE	H(wt||mu)	GCratio

A23G	-15.600	-16.000	0.400	0.877	0.336066
    ]]></help>

    <citations>
        <citation type="doi">10.1093/nar/gks1009</citation>
    </citations>
</tool>