--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnasubopt.xml	Tue Dec 06 12:37:10 2016 -0500
@@ -0,0 +1,235 @@
+<tool id="viennarna_rnasubopt" name="@EXECUTABLE@" version="@VERSION@.0">
+    <description>Calculates suboptimal secondary structures of RNAs</description>
+    <macros>
+        <token name="@EXECUTABLE@">RNAsubopt</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    RNAsubopt < '$input' > '$output'
+    -T$temperature
+    --dangles=$dangling
+    #if $methodOption.methodSelector == "range"
+        --deltaEnergy=$methodOption.deltaenergy
+    #else
+        --stochBT=$methodOption.stochastic
+    #end if
+    #if $outputOption.outputSelector == "yes"
+        --deltaEnergyPost=$deltaenergypost
+    #end if
+    $sorted
+    $dos
+    $zuker
+    #if $varExists('$advancedOptions.nolp')
+        $advancedOptions.noconversion
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.notetra
+        $advancedOptions.logml
+    #end if
+    #if $constraints.maxBPspan <> -1
+        --maxBPspan=$constraints.maxBPspan
+    #end if
+    #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
+        --constraint='$constraints.constraintLocation.constraintsFile'
+        $constraints.constraintLocation.canonicalBPonly
+        $constraints.constraintLocation.enforceConstraint
+    #end if
+    #if str($constraints.shapeOption.shapeSelector) == "isUsed"
+        --shape='$constraints.shapeOption.shapeFile'
+        #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W"
+            #set $s="W"
+            --shapeMethod=$s
+        #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "Z"
+            #set $s="Zb"+str($constraints.shapeOption.shapeMethod.b)
+            --shapeMethod=$s
+            #if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C"
+                #set $c="C"+str($constraints.shapeOption.shapeMethod.shapeConversion.c)
+                --shapeConversion=$c
+            #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L"
+                #set $c="Ls"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
+                --shapeConversion=$c
+            #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O"
+                #set $c="Os"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
+                --shapeConversion=$c
+            #else
+                #set $c=str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector)
+                --shapeConversion=$c
+            #end if
+        #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "D"
+            #set $s="Dm"+str($constraints.shapeOption.shapeMethod.m)+"b"+str($constraints.shapeOption.shapeMethod.b)
+            --shapeMethod=$s
+        #end if
+    #end if
+]]>
+    </command>
+
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta file"/>
+        <param name="temperature" 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="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
+            <option value="0">ignore dangling ends (0)</option>
+            <option value="1">unpaired bases participate in one dangling end only (1)</option>
+            <option value="3">allow coaxial stacking (3)</option>
+        </param>
+        
+        <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort the secondary structures by energy" help="--sorted"/>
+        <param name="dos" type="boolean" truevalue="--dos" falsevalue="" checked="false" label="Calculate the density of states instead of the structure" help="--dos"/>
+        <param name="zuker" type="boolean" truevalue="--zuker" falsevalue="" checked="false" label="Calculate the Zuker suboptimals instead of the structures within a range." help="--zuker"/>
+
+        <conditional name="methodOption">
+            <param name="methodSelector" type="select" label="select algorithm">
+                <option value="range" selected="true">energy range</option>
+                <option value="stochastic">choose stochastically</option>
+            </param>
+            <when value="stochastic">
+                <param name="stochastic"  type="integer" value="1" label="Calculate this number of suboptimal structures chosen stochastically" help="--stochBT"/>
+            </when>
+            <when value="range">
+                <param name="deltaenergy" type="float" optional="true" label="Range of energy for the suboptimal structures." help="--deltaEnergy"/>
+            </when>
+        </conditional>
+
+        <conditional name="outputOption">
+            <param name="outputSelector" type="select" label="select output restriction">
+                <option value="no" selected="true">no restriction</option>
+                <option value="yes">restricted output</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="deltaenergypost" type="float" value="0.0" label="Print only those structures that have a smaller difference in energy than the mfe." help="--deltaEnergyPost"/>
+            </when>
+        </conditional>
+
+        <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="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
+                <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="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="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/>                
+                <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Recalculate energies of structures using a logarithmic energy function for multi-loops" help="--logML"/>
+            </when>
+            <when value="basic">
+            </when>
+        </conditional>
+        
+        <section name="constraints" title="Structure constraints">
+            <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
+            <conditional name="constraintLocation">
+                <param name="constraintSelector" type="select" label="Constraints">
+                    <!-- <option value="fromInput">The constraints are included in the input file</option> -->
+                    <option value="fromFile">The constraints are in a seperate file</option>
+                    <option value="none" selected="true">Don't use constraints</option>
+                </param>
+            <!--	<when value="fromInput"></when> -->
+                <when value="none"></when>
+                <when value="fromFile">
+                    <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/>
+                    <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from the structure constraint" />
+                    <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
+                </when>
+            </conditional>
+            
+          <conditional name="shapeOption">
+                <param name="shapeSelector" type="select" label="Shape reactivity data">
+                    <option value="isUsed">Use shape reactivity data</option>
+                    <option value="notUsed" selected="true">Don't use shape reactivity data</option>
+                </param>
+                <when value ="isUsed">
+                    <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/>
+                    <conditional name="shapeMethod">
+                        <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod">
+                            <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option>
+                            <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option>
+                            <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option>
+                        </param>
+                        <when value="D">
+                            <param name="m" type="float" value="1.8" label="Slope m"/>
+                            <param name="b" type="float" value="-0.6" label="Intercept"/>
+                        </when>
+                        <when value="Z">
+                            <param name="b" type="float" value="-0.6" label="Intercept"/>
+                            <conditional name="shapeConversion">
+                                <param name="conversionSelector" type="select" label="shape reactivity data" argument="--shapeConversion">
+                                    <option value="M">M: Use linear mapping according to Zarringhalam et al</option>
+                                    <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option>
+                                    <option value="S">S: Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values</option>
+                                    <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option>
+                                    <option value="O" selected="true">O: Use a linear model to convert the log of the reactivity into a probability for being unpaired</option>
+                                </param>
+                                <when value="M">
+                                </when>
+                                <when value="C">
+                                    <param name="c" type="float" value="0.25" label="Cutoff"/>
+                                </when>
+                                <when value="S">
+                                </when>
+                                <when value="L">
+                                    <param name="s" type="float" value="0.68" label="Slope"/>
+                                    <param name="i" type="float" value="0.2" label="Intercept"/>
+                                </when>
+                                <when value="O">
+                                    <param name="s" type="float" value="1.6" label="Slope s"/>
+                                    <param name="i" type="float" value="-2.29" label="Intercept"/>
+                                </when>
+                            </conditional>
+                        </when>
+                        <when value="W">
+                        </when>
+                    </conditional>
+                </when>
+                <when value="notUsed">
+                </when>
+            </conditional>
+    </section>
+    </inputs>
+    <outputs>
+        <data format="txt" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="rnasubopt_input1.fa"/>
+            <output name="output" file="rnasubopt_result1.txt"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**RNAsubopt**
+
+In the default -e mode RNAsubopt calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range.
+
+Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.
+
+
+-----
+
+**Input format**
+
+RNAsubopt requires one input file
+
+- fasta file
+
+
+------
+
+**Outputs**
+
+- secondary structure in dot-bracket format
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>