Mercurial > repos > rnateam > vienna_rna
changeset 0:031ad3250176 draft
Uploaded
| author | rnateam |
|---|---|
| date | Tue, 03 Feb 2015 04:59:51 -0500 |
| parents | |
| children | b82c46050674 |
| files | macros.xml rna2dfold.xml rnaaliduplex.xml rnaalifold.xml rnacofold.xml rnadistance.xml rnaduplex.xml rnaeval.xml rnafold.xml rnaheat.xml rnainverse.xml rnalalifold.xml rnalfold.xml rnapaln.xml rnapdist.xml rnapkplex.xml rnaplex.xml rnaplfold.xml rnaplot.xml rnasnoop.xml rnasubopt.xml rnaup.xml tool_dependencies.xml |
| diffstat | 23 files changed, 2142 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,26 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.1">vienna_rna</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>@EXECUTABLE@ --version</version_command> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1186/1748-7188-6-26</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rna2dfold.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,115 @@ +<tool id="rna2dfold" name="RNA2Dfold" version="2.1.6.0"> + <description>explore structure space between two reference structures</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNA2Dfold</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNA2Dfold -T $temperature -d $dangling --stochBT=$nrbt + #if int($nk) > -1 and int($nl) > -1 + --neighborhood=$nk:$nl + #end if + #if $varExists('$pfselect.pfscaling') + --partfunc --pfScale=$pfselect.pfscaling + #end if + #if $varExists('$advancedOptions.noconversion') + #if $advancedOptions.noconversion + --noconv + #end if + #if $advancedOptions.nogu + --noGU + #end if + #if $advancedOptions.noclosinggu + --noClosingGU + #end if + #if $advancedOptions.notetra + --noTetra + #end if + --maxDist1=$maxK + --maxDist2=$maxL + #end if + < $custom_input > $out_file +]]> + </command> + <inputs> + <param format="txt" name="custom_input" type="data" label="Custom File"/> + <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/> + <param name="nrbt" type="integer" value="1" label="number of backtrack of Boltzmann samples" help="--stochBT=INT"/> + <param name="nk" type="integer" value="-1" label="k distance to first reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/> + <param name="nl" type="integer" value="-1" label="l distance to second reference structure of neighborhood in which to backtrack" help="--neighborhood=k:l"/> + <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> + <param name="circular" type="boolean" checked="false" label="assume circular RNA structure" help="--circ"/> + <conditional name="pfselect"> + <param name="pf" type="select" label="calculate partition function" help="--partfunc"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="pfscaling" size="6" type="float" value="1.0" label="scaling factor for the partition function"/> + </when> + </conditional> + + <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="maxK" type="integer" value="50" label="Maximum distance to first reference structure" help="--maxDist1=INT"/> + <param name="maxL" type="integer" value="50" label="Maximum distance to second reference structure" help="--maxDist2=INT"/> + <param name="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> + <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/> + <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> + <param name="noclosinggu" type="boolean" 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" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out_file"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNA2Dfold** + +The program partitions the secondary structure space into (basepair)distance +classes according to two fixed reference structures. It expects a sequence and +two secondary structures in dot-bracket notation as its inputs. For each +distance class, the MFE representative, Boltzmann probabilities and Gibbs free +energy is computed. Additionally, a stochastic backtracking routine allows to +produce samples of representative suboptimal secondary structures from each +partition. +The k-distance corresponds to the distance to the first reference structure, and +the l-distance corresponds to the distance to the second reference structure + +----- + +**Input format** + +RNA2Dfold requires one input file in the following format + +- 1st line: RNA sequence +- 2nd line: first reference structure in dot-bracket format +- 3rd line: second reference structure in dot-bracket format + +------ + +**Outputs** + +- text output with several secondary structures and its energies + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaaliduplex.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,92 @@ +<tool id="rnaaliduplex" name="RNAaliduplex" version="2.1.6.0"> + <description>find binding sites of two RNA alignments</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAaliduplex</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAaliduplex -T $temperature -d $dangling $flagsort --deltaEnergy=$deltaenergy $input1 $input2 + #if $varExists('$advancedOptions.noconversion') + $advancedOptions.noconversion + $advancedOptions.gquad + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if + > $out_file +]]> + </command> + <inputs> + <param format="txt" name="input1" type="data" label="Clustal alignment file"/> + <param format="txt" name="input2" type="data" label="Clustal alignment file"/> + <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/> + <param name="deltaenergy" size="6" type="float" value="0.0" label="Compute suboptimal structures with an maximal energy difference [kcal/mol] to optimum" help="--deltaEnergy=range"/> + <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> + <param name="flagsort" type="boolean" checked="false" label="Output will be sorted by free energy" truevalue="--sorted" falsevalue="" help="--sorted"/> + <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" checked="false" truevalue="--noconv" falsevalue="" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> + <param name="nogu" type="boolean" checked="false" truevalue="-noGU" falsevalue="" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> + <param name="noclosinggu" type="boolean" checked="false" truevalue="--noClosingGU" falsevalue="" 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" checked="false" truevalue="--noTetra" falsevalue="" label="No stabilization for loops, hairpins etc." help="--noTetra"/> + <param name="nolp" type="boolean" checked="false" truevalue="--noLP" falsevalue="" label="No lonely pairs (helices of length 1) will be created." help="--noLP"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out_file"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAaliduplex** + +The program reads two alignments of RNA sequences in CLUSTAL format and +predicts optimal and suboptimal binding sites, hybridization energies and the +corresponding structures. The calculation takes only inter-molecular base pairs +into account, for the general case use RNAcofold. The use of alignments allows +to focus on binding sites that are evolutionary conserved. Note, that the two +input alignments need to have an equal number of sequences and the same order, +i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc. + +The computed binding sites, energies, and structures are written to stdout, one +structure per line. Each line consist of: The structure in dot bracket format +with a & separating the two strands. The range of the structure in the two +sequences in the format "from,to : from,to"; the energy of duplex structure +in kcal/mol. +The format is especially useful for computing the hybrid structure between a +small probe sequence and a long target sequence. + + + +----- + +**Input format** + +RNAaliduplex takes two alignment files generated with Clustal (*.aln). + +------ + +**Outputs** + +- text output with several secondary structures and its energies + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaalifold.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,119 @@ +<tool id="rnaalifold" name="RNAalifold" version="2.1.6.0"> + <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAalifold</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAalifold < $input > $tabularFile + -T$temperature -d$dangling + $pf + $mis + #if $measelect.mea=="yes" + --mea=$measelect.meavalue + #end if + #if $backtrackselect.backtrack=="yes" + --stochBT_en=$backtrackselect.backtrackvalue + #end if + #if $varExists('$advancedOptions.color') + $advancedOptions.alignment + $advancedOptions.color + $advancedOptions.gquad + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + $advancedOptions.canonicalonly + $advancedOptions.circular + --cfactor=$advancedOptions.cfactor + --nfactor=$advancedOptions.nfactor + $advancedOptions.endgaps + $advancedOptions.ribosum + #end if + ; tar -cf $imagesFile *.ps +]]> + </command> + <inputs> + <param format="clustal" name="input" type="data" label="Clustal 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="-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="measelect"> + <param name="mea" type="select" label="calculate maximum expected accuracy" help="--MEA"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/> + </when> + </conditional> + <conditional name="backtrackselect"> + <param name="backtrack" type="select" label="number of structures" help="--stochBT_en"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="backtrackvalue" size="4" type="integer" value="1" label="Number of random structures."/> + </when> + </conditional> + <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="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Colored and annotated alignment image" help="--color"/> + <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image" help="--color"/> + <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"/> + <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/> + <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/> + <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="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/> + <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="tabularFile"/> + <data format="tar" name="imagesFile"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAalifold** + +----- + +**Input format** + +RNAalifold 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnacofold.xml Tue Feb 03 04:59:51 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"/> + <data format="txt" name="structure"> + <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" visible="true"/> + </data> + <data format="txt" name="dotplot"> + <filter>pf is True</filter> + <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> + </data> + </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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnadistance.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,82 @@ +<tool id="rnadistance" name="RNAdistance" version="2.1.6.0"> + <description>Calculate distance between secondary structures of two RNAs</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAdistance</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAdistance < $input > $outfile + --distance=#echo ''.join(str($distance).split(','))# + --compare=$compare + $shapiro + $backtrack + #if $backtrack and str($compare)=="m" + ; cat backtrack.file >> $outfile + #end if +]]> + </command> + + <inputs> + <param name="input" type="data" label="Primary and secondary stuctures file"/> + <param name="distance" type="select" multiple="true" display="checkboxes" label="Representation to calculate the distance / alignment option"> + <option value="f" selected="true">full/tree</option> + <option value="F">full/string</option> + <option value="h">hit/tree</option> + <option value="H">hit/string</option> + <option value="w">weighted coarse/tree</option> + <option value="W">weighted coarse/string</option> + <option value="c">coarse/tree</option> + <option value="C">coarse/string</option> + <validator type="no_options" message="Please select at least one type."/> + </param> + <param name="compare" type="select" label="Comparison Option" help="-d"> + <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option> + <option value="m">m: matrix (each with each, output in matrix form)</option> + <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option> + <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option> + </param> + <param name="shapiro" type="boolean" checked="false" truevalue="--shapiro" falsevalue="" label="Use cost matrix by Bruce Shapiro" help="--shapiro"/> + <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/> + </inputs> + <outputs> + <data format="txt" name="outfile"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAdistance** + + +----- + +**Input format** + +RNAdistance requires one input file with the following structure: +1st line: can be a comment line like in Fasta, begins with '>' +2nd line: sequence +3rd line: first secondary structure in dot-bracket notation +4th line: second secondary structure in dot-bracket notation +... +nth line: another sequence +... + +Several different RNA secondary structures can be specified. The input has a Fasta-like structure but with secondary structure information. + + +------ + +**Outputs** + +* distance of the structures +* with the backtrack options it is possible to get alignment ouput + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaduplex.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,76 @@ +<tool id="rnaduplex" name="RNAduplex" version="2.1.6.0"> + <description>Compute the structure upon hybridization of two RNA strands</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAduplex</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAduplex < $input > $tabularFile + -T$temperature -d$dangling --deltaEnergy=$denergy + #if $varExists('$advancedOptions.noconversion') + $advancedOptions.noconversion + $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="denergy" size="6" type="float" value="0.0" label="delta energy range [kcal/mol] for suboptimal structures" help="-deltaEnergy"/> + <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort by energy" help="--sorted"/> + + <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="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"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAduplex** +RNA duplex reads two RNA sequences and computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter−molecular base pairs, for the general case use RNAcofold. The computed optimal and suboptimal structure are written to stdout, one structure per line. Suboptimal structures are computed with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only. + +----- + +**Input format** + +RNAduplex requires one input file in Fasta format. The secondary strucures will be calculated pairwise: 1st sequence with 2nd sequence, 3rd sequence with 4th sequence, etc. + +------ + +**Outputs** + +Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. The format is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence. + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaeval.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,77 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnafold.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,124 @@ +<tool id="rnafold" name="RNAfold" version="2.1.6.0"> + <description>Calculate minimum free energy secondary structures and partition function of RNAs</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAfold</token> + <import>macros.xml</import> + </macros> + <command> + <![CDATA[ + RNAfold + -T $temperature + --dangles=$dangling + #if $measelect.mea == "yes": + --MEA=$measelect.meavalue + #else + $measelect.pf + #end if + #if $varExists('$advancedOptions.nogu'): + $advancedOptions.noconversion + $advancedOptions.gquad + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.canonicalonly + $advancedOptions.circular + #end if + + < $fasta_input + + > $tabular_file +]]> + </command> + + <inputs> + <param format="fasta" name="fasta_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> + <conditional name="measelect"> + <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/> + </when> + <when value="no"> + <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/> + </when> + </conditional> + <conditional name="advancedOptions"> + <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/> + <when value="true"> + <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> + <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"/> + <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/> + <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="tabular_file"/> + <data format="txt" name="structure"> + <discover_datasets pattern="(?P<designation>.+)_ss\.ps" ext="eps" visible="true"/> + </data> + <data format="txt" name="dotplot"> + <filter>measelect['pf'] is True</filter> + <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> + </data> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAfold** + +The program reads RNA sequences, calculates their minimum free +energy (mfe) structure and the mfe structure in dot-bracket notation. + +If the -p option was given it also computes the +partition function (pf) and base pairing probability matrix. + +The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing +probability in the upper right half, and one square for each pair in the +minimum free energy structure in the lower left half. For each pair i-j with +probability p>10E-6 there is a line of the form + +i j sqrt(p) ubox + +in the PostScript file, so that the pair probabilities can be easily extracted. + +The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively. +The program will read the whole FASTA input file and provide output for each found sequence. + + +----- + +**Input format** + +RNAfold requires one input file +- FASTA file + +------ + +**Outputs** + +- Secondary structures in dot-bracket notation + +- several possible postscript images bundled together in a tar file + - secondary structure for each sequence in the input file + - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence + +]]> + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaheat.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,80 @@ +<tool id="rnaheat" name="RNAheat" version="2.1.6.0"> + <description>Calculate energies of RNA in a temperature range</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAheat</token> + <import>macros.xml</import> + </macros> + <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 + #end if +]]> + </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Input file"/> + <param name="tmin" size="6" type="float" value="0.0" label="minimal temperature [°C]" help="--Tmin"/> + <param name="tmax" size="6" type="float" value="100.0" label="maximal temperature [°C]" help="--Tmax"/> + <param name="stepsize" size="6" type="float" value="1.0" label="stepsize [°C]" help="--stepsize"/> + <param name="ipoints" size="3" 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="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> + <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="output"/> + </outputs> + <tests> + </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="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnainverse.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,83 @@ +<tool id="rnainverse" name="RNAinverse" version="2.1.6.0"> + <description>Calculate RNA sequence from secondary structure</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAinverse</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAinverse < $input > $outfile + --function=#echo ''.join(str($algo).split(','))# + -R$reps + --final=$final + + #if $varExists('$advancedOptions.nogu') + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if + +]]> + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Clustal alignment file"/> + <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/> + + <param name="reps" size="6" type="integer" value="1" min="1" label="Find so many sequences that fold close to that structure" help="-R: This parameter could be negative to search for exact solutions, but in that case the program might not terminate. If you need this functionality contact your admin or run the program locally."/> + + <param name="algo" type="select" multiple="true" display="checkboxes" label="Use these functions"> + <option value="m" selected="true">minimum energy</option> + <option value="p">partition function</option> + </param> + <param name="final" size="6" type="float" value="0.0" label="If partition function is selected this value determines the convergence criterium." help="--final"/> + + <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="nogu" type="boolean" checked="false" truevalue="-noGU" falsevalue="" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> + <param name="noclosinggu" type="boolean" checked="false" truevalue="--noClosingGU" falsevalue="" 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" checked="false" truevalue="--noTetra" falsevalue="" label="No stabilization for loops, hairpins etc." help="--noTetra"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="outfile"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ +**RNAinverse** + +The program searches for sequences folding into a predefined structure, thereby inverting the folding algorithm. For each search the best sequence found and its Hamming distance to the start sequence are printed. If the the search was unsuccessful, a structure distance to the target is appended. + + +----- + +**Input format** + +Input is similar to a Fasta file. First line should be the structure in dot-bracket notation, second line the starting sequence. Lines with '>' in the beginning are treated as comments. Characters in the start sequence other than "AUGC" will be treated as wild cards and replaced by a random character. Any lower case characters in the start sequence will be kept fixed during the search. If necessary, the sequence will be elongated to the length of the structure. Thus a string of "N"s as well as a blank line specify a random start sequence. + +------ + +**Outputs** + +- text output of each sequence with its Hamming distance and/or the energy if the partition function is selected + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnalalifold.xml Tue Feb 03 04:59:51 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnalfold.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,92 @@ +<tool id="rnalfold" name="RNALfold" version="2.1.6.0"> + <description>calculates locally stable secondary structures of RNA</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNALfold</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNALfold -L $span -T $temperature -d$dangling < $fasta_input | sed -r 's/(^[.()]*) +(\(.*\)) +(.*)/\1\t\2\t\3/' > $out_file + #if $varExists('$advancedOptions.noconversion') + #if $advancedOptions.noconversion + --noconv + #end if + #if $advancedOptions.gquad + --gquad + #end if + #if $advancedOptions.nolp + --noLP + #end if + #if $advancedOptions.nogu + --noGU + #end if + #if $advancedOptions.noclosinggu + --noClosingGU + #end if + #if $advancedOptions.notetra + --noTetra + #end if + #end if +]]> + </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" 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="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="noconversion" type="boolean" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/> + <param name="gquad" type="boolean" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/> + <param name="nolp" type="boolean" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/> + <param name="nogu" type="boolean" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> + <param name="noclosinggu" type="boolean" 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" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out_file"/> + </outputs> + <tests> + </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="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnapaln.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,108 @@ +<tool id="rnapaln" name="RNApaln" version="2.1.6.0"> + <description>RNA alignment based on sequence base pairing propensities + </description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNApaln</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNApaln < $input > $output + --mode=$compare + -T$temperature -d$dangling + $backtrack + --gapo=$gapo + --gape=$gape + --seqw=$seqw + $endgaps + + #if $varExists('$advancedOptions.nolp') + $advancedOptions.nooconv + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if + + #if $backtrack and str($compare)=="m" + ; cat backtrack.file >> $outfile + #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="compare" type="select" label="Comparison Option" help="-d"> + <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option> + <option value="m">m: matrix (each with each, output in matrix form)</option> + <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option> + <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option> + </param> + + <!-- In version 2.1.2 and 2.1.7 the alignment score is wrong if -B is not selected, therefore the default for this option is set to true --> + <param name="backtrack" type="boolean" checked="true" truevalue="-B" falsevalue="" label="Print an alignment" help="-B"/> + + <param name="gapo" size="8" type="float" value="1.5" label="gap open penalty" help="--gapo"/> + <param name="gape" size="8" type="float" value="0.67" label="gap extension penalty" help="--gape"/> + <param name="seqw" size="8" type="float" value="0.5" label="weight of sequence compared to structure" help="--seqw"/> + <param name="endgaps" type="boolean" checked="false" truevalue="--endgaps" falsevalue="" label="Allow free end-gaps" help="--endgaps"/> + + <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="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/> + <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="output"/> + <data format="txt" name="dotplot"> + <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> + </data> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNApaln** + +RNA alignment based on sequence base pairing propensities. + +Uses string-alignment techniques to perform fast pairwise structural alignments of RNAs. Similar to RNApdist secondary structure is incorporated in an approximate manner by computing base pair probabilities, which are then reduced to a vector holding the probability that a base is paired upstream, downstream, or remains unpaired. Such pair propsensity vectors can then be compared using standard alignment algorithms. In contrast to RNApdist, RNApaln performs similarity (instead of distance) alignments, considers both sequence and structure information, and uses affine (rather than linear) gap costs. RNApaln can perform semi-local alignments by using free end gaps, a true local alignment mode is planned. + +----- + +**Input format** + +RNApaln requires one input file +- Fasta file + +------ + +**Outputs** + +- output of alignment scores and alignments (if -B option is selected) +- dot plot matrices in postscript format bundled together in a tar file + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnapdist.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,95 @@ +<tool id="rnapdist" name="RNApdist" version="2.1.6.0"> + <description>Calculate distances between thermodynamic RNA secondary structure ensembles + </description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNApdist</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNApdist < $input > $output + --compare=$compare + -T$temperature -d$dangling + $backtrack + + #if $varExists('$advancedOptions.nolp') + $advancedOptions.noconv + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if + + #if $backtrack and str($compare)=="m" + ; cat backtrack.file >> $outfile + #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="compare" type="select" label="Comparison Option" help="-d"> + <option value="p" selected="True">p: pairwise (1st with 2nd, 3rd with 4th, ...)</option> + <option value="m">m: matrix (each with each, output in matrix form)</option> + <option value="f" >f: first (1st with 2nd, 1st with 3rd, ...)</option> + <option value="c">c: continuous (1st with 2nd, 2nd with 3rd, ...)</option> + </param> + <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/> + <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="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/> + <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="output"/> + <data format="txt" name="dotplot"> + <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> + </data> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNApdist** + +RNApdist calculates structure distances between the thermodynamic ensembles of the secondary structures of RNA sequences. + +----- + +**Input format** + +RNApdist requires one input file +- Fasta file + +------ + +**Outputs** + +- output of alignment scores and alignments (if -B option is selected) +- dot plot matrices in postscript format bundled together in a tar file + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnapkplex.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,89 @@ +<tool id="rnapkplex" name="RNAPKplex" version="2.1.6.0"> + <description> predicts RNA secondary structures including pseudoknots</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAPKplex</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAPKplex < $input > $output + -T$temperature + --energyCutoff=$energycutoff + + #if $varExists('$advancedOptions.nolp') + --cutoff=$advancedOptions.cutoff + --subopts=$advancedOptions.suboptimal + $advancedOptions.verbose + $advancedOptions.noconv + $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="8" type="float" value="37.0" label="temperature [°C]" help="-T"/> + <param name="energycutoff" size="8" type="float" value="-8.1" label="Pseudoknots cutoff. Pseudoknots with smaller energy gains are rejected." help="--energyCutoff"/> + <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="suboptimal" size="8" type="float" value="0.0" label="Print suboptimal pseudoknots" help="--subopts"/> + <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose mode, more output" help="--verbose"/> + <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/> + <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"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output"/> + <data format="txt" name="dotplot"> + <discover_datasets pattern="(?P<designation>.+)\.ps" ext="eps" visible="true"/> + </data> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAPKplex** + +Computes RNA secondary structures by first making two sequence intervals accessible and unpaired using the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space. The algorithm furthermore always considers dangle=2 model. + +It also produces a PostScript file with a plot of the pseudoknot-free secondary structure graph, in which the bases forming the pseuodknot are marked red. + +For each structure in the Fasta input, a PostScript file is produced for the structure graph. + +----- + +**Input format** + +RNAPKplex requires one input file + +- fasta file + +The input format is similar to fasta except that even long sequences may not be interrupted by line breaks, and the header lines are optional. + +------ + +**Outputs** + +- secondary structure in dot-bracket format +- Images of the calculated structures + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaplex.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,125 @@ +<tool id="rnaplex" name="RNAplex" version="2.1.6.0"> + <description>Find targets of a query RNA</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAplex</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAplex + #if str($clustalOption.clustalFlag) == "clustal" + --alignment-mode + -q$input1 -t$input2 + #else + < $input + #end if + -T$temperature + --interaction-length=$maxLength + --extension-cost=$extensionCost + --scale-accessibility=$scaleAccessibility + $constraint + + + #if $varExists('clustalOption.meltingOption.probeConc') + --probe-mode + --probe-concentration=$clustalOption.meltingOption.probeConc + --na-concentration=$clustalOption.meltingOption.naConc + --mg-concentration=$clustalOption.meltingOption.mgConc + --k-concentration=$clustalOption.meltingOption.kConc + --tris-concentration=$clustalOption.meltingOption.trisConc + #end if + + + + #if $varExists('$advancedOptions.duplexDistance') + --fast-folding=$advancedOptions.fastFolding + --duplex-distance=$advancedOptions.duplexDistance + --energy-threshold=$advancedOptions.enThreshold + #end if + > $output +]]> + </command> + + <inputs> + <conditional name="clustalOption"> + <param name="clustalFlag" type="select" label="Input options"> + <option value="fasta" selected="true">Fasta input file</option> + <option value="clustal">Clustalw input files</option> + </param> + <when value="fasta"> + <param format="fasta" name="input" type="data" label="Fasta file"/> + <conditional name="meltingOption"> + <param name="meltingSelector" type="select" label="calculate melting temperature"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="probeConc" type="float" value="0.1" label="Concentration of the probe" help="--probe-concentration"/> + <param name="naConc" type="float" value="1.0" label="Na concentration" help="--na-concentration"/> + <param name="mgConc" type="float" value="1.0" label="Mg concentration" help="--mg-concentration"/> + <param name="kConc" type="float" value="1.0" label="K concentration" help="--k-concentration"/> + <param name="trisConc" type="float" value="1.0" label="Tris concentration" help="--tris-concentration"/> + </when> + </conditional> + </when> + <when value="clustal"> + <param format="txt" name="input1" type="data" label="Clustal file / Query sequences"/> + <param format="txt" name="input2" type="data" label="Clustal file / Target sequences"/> + </when> + </conditional> + <param name="temperature" size="8" type="float" value="37.0" label="temperature [°C]" help="-T"/> + <param name="maxLength" type="integer" min="0" value="40" label="maximal interaction length" help="--interaction-length"/> + <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/> + <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/> + <param name="scaleAccessibility" size="8" type="float" value="1.0" label="scale all opening energy by a factor" help="--scale-accessibility"/> + <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints. Constraints have to be given in the input file" help="--constraint"/> + + <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="fastFolding" type="select" label="Backtracking" help="--fast-folding"> + <option value="0" selected="true">based on standard energy model (0) - normal</option> + <option value="2">based on approximate plex model (2) - faster</option> + <option value="1">no recomputation (1) - fastest</option> + </param> + <param name="duplexDistance" type="integer" value="0" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/> + <param name="enThreshold" size="8" type="float" value="-100000" label="Minimum Energy Gain for a Duplex [kcal/mol]" help="--energy-threshold"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAplex** + +Computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter-molecular base pairs. + + +----- + +**Input format** + +RNALplex requires either one Fasta file or two Clustal files as input + +------ + +**Outputs** + +The computed optimal and suboptimal structure are given, one structure per line. Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaplfold.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,110 @@ +<tool id="rnaplfold" name="RNAplfold" version="2.1.6.0"> + <description> predicts RNA secondary structures including pseudoknots</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAplfold</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAplfold < $input + -T$temperature + --dangles=$dangling + --cutoff=$cutoff + --winsize=$winsize + --span=$span + $onthefly + $openingenergies + #if $varExists('$unpairedOption.ulength') + --ulength=$unpairedOption.ulength + #end if + + #if $varExists('$advancedOptions.nolp') + $advancedOptions.noconv + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if + ;ls *_basepairs *_lunp *_openen > files.tmp + ;tar -cf $outputf --files-from=files.tmp + +]]> + </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Fasta file"/> + <param name="temperature" size="8" 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> + <param name="winsize" type="integer" value="70" label="Average pairing probabilities over this windowsize" help="--winsize"/> + <param name="span" type="integer" value="70" label="Maximum seperation between base pairs" help="--span, -L"/> + <param name="cutoff" size="8" type="float" value="0.01" label="Cutoff probability for report on base pairing" help="--cutoff"/> + <param name="onthefly" type="boolean" truevalue="--print_onthefly" falsevalue="" checked="false" label="Print simplified base pair probabilities (_basepairs output)" help="--print_onthefly"/> + <param name="openingenergies" type="boolean" truevalue="--opening_energies" falsevalue="" checked="false" label="Output in logarithm of the probabilities (_openen output)" help="--opening_energies"/> + <conditional name="unpairedOption"> + <param name="unpairedSelector" type="select" label="Compute probabilty that region is unpaired (_lunp output)"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="ulength" type="integer" value="31" label="Maximal lenght of unpaired region" help="--ulength"/> + </when> + </conditional> + <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="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/> + <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="dotplot"> + <discover_datasets pattern="(?P<designation>.+)_dp\.ps" ext="rna_eps" visible="true"/> + </data> + <data format="tar" name="outputf"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAplfold** + +Computes local pair probabilities for base pairs with a maximal span of L. The probabilities are averaged over all windows of size L that contain the base pair. For a sequence of length n and a window size 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 stable RNA structures. + + +----- + +**Input format** + +RNAPplfold requires one input file + +- Fasta file + +------ + +**Outputs** + +For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags. +The Dot Plot Matrices are stored in a Postscript file. +The other output is packed in a tar file. + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaplot.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,78 @@ +<tool id="rnaplot" name="RNAplot" version="2.1.6.0"> + <description> Draw RNA Secondary Structures </description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAplot</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAplot < $input + --layout-type=$layoutSelector + --output-format=$formatOptions.formatSelector + #if str($formatOptions.formatSelector) == "ps" + --pre=$formatOptions.pre + --post=$formatOptions.post + ; tar -cf $imagesFile *.ps + #elif str($formatOptions.formatSelector) == "gml" + ; tar -cf $imagesFile *.gml + #elif str($formatOptions.formatSelector) == "svg" + ; tar -cf $imagesFile *.svg + #else + ; tar -cf $imagesFile *.ss + #end if +]]> + </command> + <inputs> + <param format="txt" name="input" type="data" label="Fasta file"/> + <param name="layoutSelector" type="select" label="Layout selection"> + <option value="0">Radial Layout</option> + <option value="1" selected="true">Naview Layout</option> + </param> + <conditional name="formatOptions"> + <param name="formatSelector" type="select" label="Output format selection" help="--output-format"> + <option value="ps" selected="true">Postscript (.ps)</option> + <option value="gml">Graph Meta Language (.gml)</option> + <option value="svg">Scalable Vector Graphics (.svg)</option> + <option value="xrna">XRNA Save File (.ss)</option> + </param> + <when value="ps"> + <param name="pre" size="200" type="text" label="Add annotation macros to postscript file" help="--pre"/> + <param name="post" size="200" type="text" label="Add annotations to postscript file" help="--post"/> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tar" name="imagesFile"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAplot** + +The program reads RNA sequences and structures in the format as produced by RNAfold and produces drawings of the secondary structure graph. The coordinates are produced using either E. Bruccoleri's naview routines, or a simple radial layout method. + +----- + +**Input format** + +RNAplot requires one input file + +- Fasta file with an additional line with structure information in dot-bracket notation + +------ + +**Outputs** + +- several possible postscript images bundled together in a tar file + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnasnoop.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,131 @@ +<tool id="rnasnoop" name="RNAsnoop" version="2.1.6.0"> + <description> Find targets of a query H/ACA snoRNA</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAsnoop</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAsnoop --query=$input1 --target=$input2 > $output + --alignmentLenght=$length + $constraint + --energy-threshold=$energyThreshold + #if $varExists('$advancedOptions.extensioncost') + $advancedOptions.fast + --extension-cost=$advancedOptions.extensioncost + --minimal-right-duplex=$advancedOptions.minrightduplex + --minimal-loop-energy=$advancedOptions.minloop + --minimal-left-duplex=$advancedOptions.minleftduplex + --minimal-duplex=$advancedOptions.minduplex + --duplex-distance=$advancedOptions.duplexdist + --minimal-stem-length=$advancedOptions.minstemlength + --maximal-stem-length=$advancedOptions.maxstemlength + --minimal-duplex-box-length=$advancedOptions.minbox + --maximal-duplex-box-length=$advancedOptions.maxbox + --minimal-snoRNA-stem-loop-length=$advancedOptions.minsnornastem + --maximal-snoRNA-stem-loop-length=$advancedOptions.maxsnornastem + --minimal-snoRNA-duplex-length=$advancedOptions.minsnornaduplex + --maximal-snoRNA-duplex-length=$advancedOptions.maxsnornaduplex + --minimal-duplex-stem-energy=$advancedOptions.minduplexstem + --minimal-total-energy=$advancedOptions.mintotal + --maximal-stem-asymmetry=$advancedOptions.maxstemasymmetry + --minimal-lower-stem-energy=$advancedOptions.minstemenergy + #end if + #if $filetypeOptions.filetypeSelector == "fasta" + ; tar -cf $imagesFile *.ps + #else + --alignment-mode + #end if +]]> + </command> + + <inputs> + <conditional name="filetypeOptions"> + <param name="filetypeSelector" type="select" label="Select Filetype"> + <option value="fasta" selected="true">Fasta</option> + <option value="clustal">Clustal</option> + </param> + <when value="fasta"> + <param format="fasta" name="input1" type="data" label="Query sequences"/> + <param format="fasta" name="input2" type="data" label="Target sequences"/> + </when> + <when value="clustal"> + <param format="txt" name="input1" type="data" label="Query sequences"/> + <param format="txt" name="input2" type="data" label="Target sequences"/> + </when> + </conditional> + + + <param name="length" type="integer" min="0" value="25" label="Maximal alignment length" help="--alignmentLength"/> + <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate the stem structure subject to constraints" help="--constraint"/> + <param name="energyThreshold" size="8" type="float" value="-1.0" label="Maximal energy difference between the mfe and the desired suboptimal structure" help="--energy-threshold"/> + + <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="fast" type="boolean" truevalue="--fast-folding=1" falsevalue="--fast-folding=0" checked="true" label="Backtracking based on the standard energy model" help="--fast-folding"/> + <param name="extensioncost" type="integer" value="0" label="Cost to add each nucleotide in a duplex" help="--extension-cost"/> + <param name="minrightduplex" type="integer" value="-270" label="Minimal right duplex energy" help="--minimal-right-duplex"/> + <param name="minloop" type="integer" value="-280" label="Minimal Loop energy" help="--minimal-loop-energy"/> + <param name="minleftduplex" type="integer" value="-170" label="Minimal left duplex energy" help="--minimal-left-duplex"/> + <param name="minduplex" type="integer" value="-1090" label="Minimal duplex energy" help="--minimal-duplex"/> + <param name="duplexdist" type="integer" value="2" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/> + <param name="minstemlength" type="integer" value="5" label="Minimal snoRNA stem length" help="--minimal-stem-length"/> + <param name="maxstemlength" type="integer" value="120" label="Maximal snoRNA stem length" help="--maximal-stem-length"/> + <param name="minbox" type="integer" value="11" label="Minimal distance between the duplex end and the H/ACA box" help="--minimal-duplex-box-length"/> + <param name="maxbox" type="integer" value="16" label="Maximal distance between the duplex end and the H/ACA box" help="--maximal-duplex-box-length"/> + <param name="minsnornastem" type="integer" value="1" label="Minimal distance between the stem loop and the snoRNA sequence" help="--minimal-snoRNA-stem-loop-length"/> + <param name="maxsnornastem" type="integer" value="100000" label="Maximal distance between the stem loop and the snoRNA sequence" help="--maximal-snoRNA-stem-loop-length"/> + <param name="minsnornaduplex" type="integer" value="0" label="Minimal distance between the duplex and the snoRNA sequence" help="--minimal-snoRNA-duplex-length"/> + <param name="maxsnornaduplex" type="integer" value="0" label="Maximal distance between the duplex and the snoRNA sequence" help="--maximal-snoRNA-duplex-length"/> + <param name="minduplexstem" type="integer" value="-1370" label="Minimal duplex stem energy" help="--minimal-duplex-stem-energy"/> + <param name="mintotal" type="integer" value="100000" label="Minimal total energy" help="--minimal-total-energy"/> + <param name="maxstemasymmetry" type="integer" value="30" label="Maximal snoRNA stem asymmetry" help="--maximal-stem-asymmetry"/> + <param name="minstemenergy" type="integer" value="100000" label="Minimal lower stem energy" help="--minimal-lower-stem-energy"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output"/> + <data format="tar" name="imagesFile"> + <filter>filetypeOptions['filetypeSelector'] == "fasta"</filter> + </data> + + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAsnoop** + +reads a target RNA sequence and a H/ACA snoRNA sequence from a target and query file, respectively and computes optimal and suboptimal secondary structures for their hybridization. The calculation can be done roughly done in O(nm), where is n the length of the target sequence and m is the length of the snoRNA stem, as it is specially tailored to the special case of H/ACA snoRNA. For general purpose target predictions, please have a look at RNAduplex, RNAup, RNAcofold and RNAplex. + + +----- + +**Input format** + +RNAsnoop requires two input files + +- either two Fasta files +- or two Clustal alignment files + +------ + +**Outputs** + +The computed optimal and suboptimal structure are given, one structure per line. Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The '<>' brackets represent snoRNA intramolecular interactions, while the '()' brackets represent intermolecular interactions between the snoRNA and its target. +The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. If available the opening energy are also returned. + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnasubopt.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,126 @@ +<tool id="rnasubopt" name="RNAsubopt" version="2.1.6.0"> + <description>Calculates suboptimal secondary structures of RNAs</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAsubopt</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAsubopt < $input > $output + -T$temperature + --dangles=$dangling + #if $methodOption.methodSelector == "range" + --deltaEnergy=$methodOption.deltaenergy + #else + --stochBT=$methodOption.stochastic + #end if + #if $outputOption.outputSelector == "yes" + --deltaEnergyPost=$deltaenergypost + #end if + $constraint + $sorted + $dos + $zuker + #if $varExists('$advancedOptions.nolp') + $advancedOptions.noconv + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + $advancedOptions.logml + #end if +]]> + </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Fasta file"/> + <param name="temperature" size="8" 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> + <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Constraints for the secondary structure" help="--constraint"/> + <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort the secondary structures by energy" help="--sorted"/> + <param name="dos" type="boolean" truevalue="--dos" falsevalue="" checked="false" label="Calculate the density of states instead of the structure" help="--dos"/> + <param name="zuker" type="boolean" truevalue="--zuker" falsevalue="" checked="false" label="Calculate the Zuker suboptimals instead of the structures within a range." help="--zuker"/> + + <conditional name="methodOption"> + <param name="methodSelector" type="select" label="select algorithm"> + <option value="range" selected="true">energy range</option> + <option value="stochastic">choose stochastically</option> + </param> + <when value="stochastic"> + <param name="stochastic" type="integer" value="1" label="Calculate this number of suboptimal structures chosen stochastically" help="--stochBT"/> + </when> + <when value="range"> + <param name="deltaenergy" size="8" type="float" value="1.0" label="Range of energy for the suboptimal structures." help="--deltaEnergy"/> + </when> + </conditional> + + <conditional name="outputOption"> + <param name="outputSelector" type="select" label="select output restriction"> + <option value="no" selected="true">no restriction</option> + <option value="yes">restricted output</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="deltaenergypost" size="8" type="float" value="0.0" label="Print only those structures that have a smaller difference in energy than the mfe." help="--deltaEnergyPost"/> + </when> + </conditional> + + <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="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/> + <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/> + <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="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Recalculate energies of structures using a logarithmic energy function for multi-loops" help="--logML"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAsubopt** + +In the default -e mode RNAsubopt calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range. + +Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures. + + +----- + +**Input format** + +RNAsubopt requires one input file + +- fasta file + + +------ + +**Outputs** + +- secondary structure in dot-bracket format + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnaup.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,117 @@ +<tool id="rnaup" name="RNAup" version="2.1.6.0"> + <description>Calculate the thermodynamics of RNA-RNA interactions</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <expand macro="stdio" /> + <macros> + <token name="@EXECUTABLE@">RNAup</token> + <import>macros.xml</import> + </macros> + <command> +<![CDATA[ + RNAup < $input > $output + -T$temperature + --dangles=$dangling + $constraint + --ulength=$ulength + --contributions=#echo ''.join(str($contributions).split(','))# + --window=$window + $includeboth + $interactionpairwise + $interactionfirst + --extend5=$extendfive + --extend3=$extendthree + + #if $varExists('$advancedOptions.nolp') + --pfScale=$advancedOptions.pfscale + $advancedOptions.noconv + $advancedOptions.nolp + $advancedOptions.nogu + $advancedOptions.noclosinggu + $advancedOptions.notetra + #end if + ; tar -cf $accesibilitiesFile *.out +]]> + </command> + + <inputs> + <param format="fasta" name="input" type="data" label="Fasta file"/> + <param name="temperature" size="8" 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> + <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Constraints for the secondary structure" help="--constraint"/> + <param name="ulength" type="integer" min="0" value="4" label="Length of the unstructured region." help="--ulength"/> + <param name="contributions" type="select" multiple="true" display="checkboxes" label="Specify which contributions to the probabilty of being unpaired are listed in the output"> + <option value="S" selected="true">sum of all</option> + <option value="H">unpaired within hairpin loop</option> + <option value="I">unpaired within interior loop</option> + <option value="M">unpaired within multiloop</option> + <option value="E">unpaired within exterior loop</option> + <validator type="no_options" message="Please select at least one contribution."/> + </param> + <param name="window" type="integer" min="0" value="25" label="Maximal length of the region of interaction." help="--window"/> + <param name="includeboth" type="boolean" truevalue="--include_both" falsevalue="" checked="false" label="Include the probability of unpaired regions in both RNAs" help="--include_both"/> + <param name="interactionpairwise" type="boolean" truevalue="--interaction_pairwise" falsevalue="" checked="false" label="Activate pairwise interaction mode" help="--interaction_pairwise"/> + <param name="interactionfirst" type="boolean" truevalue="--interaction_first" falsevalue="" checked="false" label="Activate pairwise interaction mode, compare always with the first sequence" help="--interaction_first"/> + <param name="extendfive" type="integer" min="0" value="0" label="Extend the region of interaction in the target to some residues on the 5' side." help="--extend5"/> + <param name="extendthree" type="integer" min="0" value="0" label="Extend the region of interaction in the target to some residues on the 3' side." help="--extend3"/> + + <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="pfscale" type="float" value="1.07" label="Use scale*mfe as an estimate for the ensemble free energy " help="--pfScale"/> + <param name="noconv" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="No conversion of T -> U" help="--noconv"/> + <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="output"/> + <data format="tar" name="accesibilitiesFile"/> + </outputs> + <tests> + </tests> + <help> +<![CDATA[ + +**RNAup** + +RNAup calculates the thermodynamics of RNA−RNA interactions, by decomposing the binding into two stages. (1) First the probability that a potential binding sites remains unpaired (equivalent to the free energy needed to open the site) is computed. (2) Then this accessibility is combined with the interaction energy to obtain the total binding energy. All calculations are done by computing partition functions over all possible conformations. + +RNAup provides two different modes: By default RNAup computes accessibilities, in terms of the free energies needed to open a region (default length 4). It prints the region of highest accessibility and its opening energy to stdout, opening energies for all other regions are written to a file. + +In interaction mode the interaction between two RNAs is calculated. It is invoked if the input consists of two sequences concatenated with an "&". RNAup assumes that the longer RNA is a structured target sequence while the shorter one is an unstructured small RNA. Additionally, for every position along the target sequence the best free energy of binding for an interaction that includes this position is written to the the output file. Output to stdout consists of the location and free energy, dG, for the optimal region of interaction. The binding energy dG is also split into its components the interaction energy dGint and the opening energy dGu_l (and possibly dGu_s for the shorter sequence). +In addition we print the optimal interaction structure as computed by RNAduplex for this region. Note that it can happen that the RNAduplex computed optimal interaction does not coincide with the optimal RNAup region. If the two predictions don’t match the structure string is replaced by a run of ".". + +----- + +**Input format** + +RNAup requires one input file + +- Fasta file + +For the interaction mode, the sequences of the query and target have to be concatenated by an '&', or the --interaction-pairwise or --interaction-first flags have to be set. + +------ + +**Outputs** + +- most accesible region of each sequence +- accesibilties of each sequence is written in a file and these files are bundled together in a tar file + + +]]> + </help> + <expand macro="requirements" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Feb 03 04:59:51 2015 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="vienna_rna" version="2.1"> + <repository changeset_revision="a169544ea199" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>