Mercurial > repos > rnateam > vienna_rna
view rnaheat.xml @ 2:5e58cbf27a05 draft
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author | rnateam |
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date | Mon, 09 Feb 2015 13:26:11 -0500 |
parents | 78d673470d45 |
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<tool id="rnaheat" name="RNAheat" version="2.1.6.0"> <description>Calculate energies of RNA in a temperature range</description> <expand macro="requirements" /> <expand macro="version_command" /> <expand macro="stdio" /> <macros> <token name="@EXECUTABLE@">RNAheat</token> <import>macros.xml</import> </macros> <command> <![CDATA[ RNAheat < $input > $output --Tmin $tmin --Tmax $tmax -d$dangling --stepsize=$stepsize --ipoints=$ipoints #if $varExists('$advancedOptions.noconversion') $advancedOptions.noconversion $advancedOptions.nolp $advancedOptions.nogu $advancedOptions.noclosinggu $advancedOptions.notetra #end if ]]> </command> <inputs> <param format="fasta" name="input" type="data" label="Input file"/> <param name="tmin" size="6" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/> <param name="tmax" size="6" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/> <param name="stepsize" size="6" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/> <param name="ipoints" size="3" type="integer" value="2" label="data points to fit parabola to: 2*value+1" help="--ipoints"/> <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 conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/> <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/> </when> </conditional> </inputs> <outputs> <data format="txt" name="output"/> </outputs> <tests> <test> <param name="input" value="rnaheat_input1.fa"/> <output name="out_file" file="rnaheat_result1.txt"/> </test> </tests> <help> <![CDATA[ **RNAheat** Calculates the specific heat of RNA sequences in the temperature range t1 to t2, from the partition function by numeric differentiation. The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve. ----- **Input format** RNAheat requires one input file Fasta format. ------ **Outputs** The result is written as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K) for each sequence in the input file. ]]> </help> <expand macro="requirements" /> </tool>