Mercurial > repos > rnateam > veinnarna_rnaeval
diff rnaeval.xml @ 0:238cf510c24f draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
| author | rnateam |
|---|---|
| date | Wed, 05 Oct 2016 04:58:30 -0400 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaeval.xml Wed Oct 05 04:58:30 2016 -0400 @@ -0,0 +1,158 @@ +<tool id="veinnarna_rnaeval" name="@EXECUTABLE@" version="@VERSION@.0"> + <description>Calculate energy of RNA sequences with given secondary structure</description> + <macros> + <token name="@EXECUTABLE@">RNAeval</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> +<![CDATA[ + RNAeval < '$input' > '$tabularFile' + -T$temperature -d$dangling + #if $varExists('$advancedOptions.noconversion') + $advancedOptions.noconversion + $advancedOptions.verbose + $advancedOptions.gquad + $advancedOptions.circ + $advancedOptions.logml + $advancedOptions.notetra + #if str($advancedOptions.shapeOption.shapeSelector) == "isUsed" + --shape='$advancedOptions.shapeOption.shapeFile' + #if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "W" + #set $s="W" + --shapeMethod=$s + #else if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "Z" + #set $s="Zb"+str($advancedOptions.shapeOption.shapeMethod.b) + --shapeMethod=$s + #if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C" + #set $c="C"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.c) + --shapeConversion=$c + #else if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L" + #set $c="Ls"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($advancedOptions.shapeOption.shapeMethod.shapeConversion.i) + --shapeConversion=$c + #else if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O" + #set $c="Os"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($advancedOptions.shapeOption.shapeMethod.shapeConversion.i) + --shapeConversion=$c + #else + #set $c=str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) + --shapeConversion=$c + #end if + #else if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "D" + #set $s="Dm"+str($advancedOptions.shapeOption.shapeMethod.m)+"b"+str($advancedOptions.shapeOption.shapeMethod.b) + --shapeMethod=$s + #end if + #end if + #end if +]]> + </command> + <inputs> + <param format="txt,dbn" name="input" type="data" label="Input 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="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="basic">basic Options</option> + <option value="advanced">advanced Options</option> + </param> + <when value="advanced"> + <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No converstion from T->U" help="--noconv"/> + <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Print out energy of each loop in the structure." help="--verbose"/> + <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G-quadruplex formation prediction" help="--gquad"/> + <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA" help="--circ"/> + <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops" help="--logML"/> + <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/> + <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"> + <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> + </when> + <when value="basic"> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="tabularFile"/> + </outputs> + <tests> + <test> + <param name="input" value="rnaeval_input1.dbn"/> + <output name="out_file" file="rnaeval_result1.txt"/> + </test> + </tests> + <help> +<![CDATA[ +**RNAeval** +RNAeval evaluates the free energy of an RNA molecule in fixed secondary structure. Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written to stdout. + +----- + +**Input format** + +RNAeval requires one input file in a format similar to the Fasta format. The secondary strucures should be added after the sequence in dot-bracket notation. Sequence and structure can be interupted by an '&' to calculate the co-folding of two RNA-strands. + + +------ + +**Outputs** + +First line: the sequence, second line: the structure with its corresponding energy + + +]]> + </help> + <expand macro="citations" /> +</tool>