Mercurial > repos > rnateam > viennarna_rnaheat
diff rnaheat.xml @ 0:b885d4fab5d4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author | rnateam |
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date | Tue, 06 Dec 2016 12:31:31 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaheat.xml Tue Dec 06 12:31:31 2016 -0500 @@ -0,0 +1,90 @@ +<tool id="viennarna_rnaheat" name="@EXECUTABLE@" version="@VERSION@.0"> + <description>Calculate energies of RNA in a temperature range</description> + <macros> + <token name="@EXECUTABLE@">RNAheat</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <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 + #if $advancedOptions.nsp + --nsp='$advancedOptions.nsp' + #end if + #end if +]]> + </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Input file"/> + <param name="tmin" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/> + <param name="tmax" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/> + <param name="stepsize" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/> + <param name="ipoints" 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="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 argument="--nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs." + help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." /> + </when> + <when value="basic"> + </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="citations" /> +</tool>