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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
author | rnateam |
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date | Wed, 20 Dec 2017 08:32:26 -0500 |
parents | a59547093b10 |
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<tool id="viennarna_rnalfold" name="@EXECUTABLE@" version="@VERSION@.0"> <description>calculates locally stable secondary structures of RNA</description> <macros> <token name="@EXECUTABLE@">RNALfold</token> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ RNALfold -L $span -T $temperature -d$dangling < '$fasta_input' #if $varExists('$advancedOptions.noconversion') $advancedOptions.noconversion $advancedOptions.gquad $advancedOptions.nolp $advancedOptions.nogu $advancedOptions.noclosinggu $advancedOptions.notetra #if $advancedOptions.activateZscore #if str($advancedOptions.zscore) <> "" --zscore=$advancedOptions.zscore #else --zscore #end if #end if #end if | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > '$out_file' ]]> </command> <inputs> <param format="fasta" name="fasta_input" type="data" label="FASTA file"/> <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/> <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="2" selected="true">unpaired bases participate in all dangling ends (2)</option> <option value="0">ignore dangling ends (0)</option> <option value="1">unpaired bases participate in one dangling end only (1)</option> <option value="3">allow coaxial stacking (3)</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="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="Take G Quadruplex formation into account" argument="-g"/> <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 name="activateZscore" type="boolean" checked="false" label="Activate Z−score computation. An optional argument may be supplied to set the threshold" help="(--zscore)"/> <param name="zscore" type="float" value="-2" optional="true" label="Z-score" help="An optional argument may be supplied to set the threshold"/> </when> <when value="basic"> </when> </conditional> </inputs> <outputs> <data format="txt" name="out_file"/> </outputs> <tests> <test> <param name="fasta_input" value="rnalfold_input1.fa"/> <output name="out_file" file="rnalfold_result1.txt"/> </test> </tests> <help> <![CDATA[ **RNALfold** Compute 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 structures*. Output consists of a list of secondary structure components of size <= L, one entry per line. Each output line contains the predicted local structure its energy in kcal/mol and the starting position of the local structure. ----- **Input format** - RNALfold requires one input file in FASTA format ------ **Outputs** - text output with dot-bracket notation and free energies of the secondary structures ]]> </help> <expand macro="citations" /> </tool>