Mercurial > repos > rnateam > viennarna_rnasubopt
diff rnasubopt.xml @ 0:58fe85fe08be draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
| author | rnateam |
|---|---|
| date | Tue, 06 Dec 2016 12:37:10 -0500 |
| parents | |
| children | 685d5971df5b |
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--- /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>