Mercurial > repos > rnateam > vienna_rna
diff rnalalifold.xml @ 0:78d673470d45 draft
Imported from capsule None
author | rnateam |
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date | Wed, 04 Feb 2015 12:05:27 -0500 |
parents | |
children | 5e58cbf27a05 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnalalifold.xml Wed Feb 04 12:05:27 2015 -0500 @@ -0,0 +1,98 @@ +<tool id="rnalalifold" name="RNALalifold" version="2.1.6.0"> + <description>Calculate locally stable secondary structures for a set of aligned RNAs</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNALalifold</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNALalifold $input > $output + -T$temperature -d$dangling + -L$span + $mis + + #if $varExists('$advancedOptions.nolp') + --cutoff=$advancedOptions.cutoff + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + --cfactor=$advancedOptions.cfactor + --nfactor=$advancedOptions.nfactor + $advancedOptions.ribosum + #end if + <!--; tar -cf $imagesFile *.ps --> +]]> + </command> + + <inputs> + <param format="clustal" name="input" type="data" label="Clustal file"/> + <param name="span" type="integer" min="0" max="5000" value="60" label="base pair span" help="Maximal distance between two paired bases. (-L)"/> + + <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> + + <!-- the -p option led to segmentation faults with version 2.1.2 and 2.1.7 --> + <!--<param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>--> + + <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/> + + <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="cutoff" type="float" value="0.01" label="cutoff probability for the reporting of the base pairs in the dot plot" help="--cutoff"/> + <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"/> + <param name="cfactor" size="6" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/> + <param name="nfactor" size="6" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/> + <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output" /> + <!-- the program does not seem to generate a dot plot, even though that is implied in the help --> + <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>--> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNALalifold** + +Calculates locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short RNA + + +----- + +**Input format** + +RNALalifold requires one input file +- Clustal file + +------ + +**Outputs** + +- energy of the consensus structures in the clustal file +- several possible postscript images bundled together in a tar file + + +]]> + </help> + <expand macro="requirements" /> +</tool>