Mercurial > repos > rnateam > vienna_rna
diff rnacofold.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/rnacofold.xml Wed Feb 04 12:05:27 2015 -0500 @@ -0,0 +1,93 @@ +<tool id="rnacofold" name="RNAcofold" version="2.1.6.0"> + <description>Calculate secondary structures of two RNAs with dimerization</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAcofold</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAcofold < $input > $tabularFile + -T$temperature -d$dangling + $pf + $allpf + #if $varExists('$advancedOptions.noconversion') + $advancedOptions.constraint + $advancedOptions.noconversion + $advancedOptions.gquad + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if +]]> + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Fasta 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> + <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/> + <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers" help="--all_pf"/> + <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="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structure subject to constraints" help="--constraint"/> + <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion T->U" help="--noconv"/> + <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/> + <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="tabularFile"/> + <collection name="sequence_outputs" type="list" label="rna_eps outputs"> + <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" /> + </collection> + <collection name="matrix_outputs" type="list" label="rna_eps outputs"> + <filter>pf is True</filter> + <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> + </collection> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAcofold** + + +----- + +**Input format** + +RNAcofold requires one input file: + +- Fasta file + +Two different RNA sequences can be specified concatenated with the '&' character. The folding of the two sequences with each other will be calculated. + + +------ + +**Outputs** + +- Energies of the RNA sequences and the dimers +- Structure images +- Dot Plot Matrix images (if --partfunc is used) + +]]> + </help> + <expand macro="requirements" /> +</tool>