Mercurial > repos > rnateam > vienna_rna
view rnaeval.xml @ 0:78d673470d45 draft
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author | rnateam |
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date | Wed, 04 Feb 2015 12:05:27 -0500 |
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children | 5e58cbf27a05 |
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<tool id="rnaeval" name="RNAeval" version="2.1.6.0"> <description>Calculate energy of RNA sequences with given secondary structure</description> <expand macro="requirements" /> <expand macro="version_command" /> <expand macro="stdio" /> <macros> <token name="@EXECUTABLE@">RNAeval</token> <import>macros.xml</import> </macros> <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 #end if ]]> </command> <inputs> <param format="text" name="input" type="data" label="Input file"/> <param name="temperature" size="6" 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"/> </when> </conditional> </inputs> <outputs> <data format="txt" name="tabularFile"/> </outputs> <tests> </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="requirements" /> </tool>