# HG changeset patch
# User rnateam
# Date 1423069527 18000
# Node ID 78d673470d45f7d22d1d4205c93a9de05b6c8b1e
Imported from capsule None
diff -r 000000000000 -r 78d673470d45 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,26 @@
+
+
+
+ vienna_rna
+
+
+
+
+ @EXECUTABLE@ --version
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1186/1748-7188-6-26
+
+
+
diff -r 000000000000 -r 78d673470d45 rna2dfold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rna2dfold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,115 @@
+
+ explore structure space between two reference structures
+
+
+
+
+ RNA2Dfold
+ macros.xml
+
+
+ -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
+]]>
+
+
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diff -r 000000000000 -r 78d673470d45 rnaaliduplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaaliduplex.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,92 @@
+
+ find binding sites of two RNA alignments
+
+
+
+
+ RNAaliduplex
+ macros.xml
+
+
+ $out_file
+]]>
+
+
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diff -r 000000000000 -r 78d673470d45 rnaalifold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaalifold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,119 @@
+
+ Calculate minimum free energy secondary structures and partition function on a multiple alignment file
+
+
+
+
+ RNAalifold
+ macros.xml
+
+
+ $tabularFile
+ -T$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
+]]>
+
+
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diff -r 000000000000 -r 78d673470d45 rnacofold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnacofold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,93 @@
+
+ Calculate secondary structures of two RNAs with dimerization
+
+
+
+
+ RNAcofold
+ macros.xml
+
+
+ $tabularFile
+ -T$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
+]]>
+
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+ pf is True
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+
+
diff -r 000000000000 -r 78d673470d45 rnadistance.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnadistance.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,82 @@
+
+ Calculate distance between secondary structures of two RNAs
+
+
+
+
+ RNAdistance
+ macros.xml
+
+
+ $outfile
+ --distance=#echo ''.join(str($distance).split(','))#
+ --compare=$compare
+ $shapiro
+ $backtrack
+ #if $backtrack and str($compare)=="m"
+ ; cat backtrack.file >> $outfile
+ #end if
+]]>
+
+
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+
+'
+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
+
+
+]]>
+
+
+
diff -r 000000000000 -r 78d673470d45 rnaduplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaduplex.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,76 @@
+
+ Compute the structure upon hybridization of two RNA strands
+
+
+
+
+ RNAduplex
+ macros.xml
+
+
+ $tabularFile
+ -T$temperature -d$dangling --deltaEnergy=$denergy
+ #if $varExists('$advancedOptions.noconversion')
+ $advancedOptions.noconversion
+ $advancedOptions.nolp
+ $advancedOptions.nogu
+ $advancedOptions.noclosinggu
+ $advancedOptions.notetra
+ #end if
+]]>
+
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diff -r 000000000000 -r 78d673470d45 rnaeval.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaeval.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,77 @@
+
+ Calculate energy of RNA sequences with given secondary structure
+
+
+
+
+ RNAeval
+ macros.xml
+
+
+ $tabularFile
+ -T$temperature -d$dangling
+ #if $varExists('$advancedOptions.noconversion')
+ $advancedOptions.noconversion
+ $advancedOptions.verbose
+ $advancedOptions.gquad
+ $advancedOptions.circ
+ $advancedOptions.logml
+ $advancedOptions.notetra
+ #end if
+]]>
+
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diff -r 000000000000 -r 78d673470d45 rnafold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnafold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,125 @@
+
+ Calculate minimum free energy secondary structures and partition function of RNAs
+
+
+
+
+ RNAfold
+ macros.xml
+
+
+ $tabular_file
+]]>
+
+
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+ measelect['pf'] is True
+
+
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+
+
+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
+
+]]>
+
+
+
diff -r 000000000000 -r 78d673470d45 rnaheat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaheat.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,80 @@
+
+ Calculate energies of RNA in a temperature range
+
+
+
+
+ RNAheat
+ macros.xml
+
+
+ $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
+]]>
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diff -r 000000000000 -r 78d673470d45 rnainverse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnainverse.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,83 @@
+
+ Calculate RNA sequence from secondary structure
+
+
+
+
+ RNAinverse
+ macros.xml
+
+
+ $outfile
+ --function=#echo ''.join(str($algo).split(','))#
+ -R$reps
+ --final=$final
+
+ #if $varExists('$advancedOptions.nogu')
+ $advancedOptions.nogu
+ $advancedOptions.noclosinggu
+ $advancedOptions.notetra
+ #end if
+
+]]>
+
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+
+' 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
+
+]]>
+
+
+
diff -r 000000000000 -r 78d673470d45 rnalalifold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnalalifold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,98 @@
+
+ Calculate locally stable secondary structures for a set of aligned RNAs
+
+
+
+
+ RNALalifold
+ macros.xml
+
+
+ $output
+ -T$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
+
+]]>
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diff -r 000000000000 -r 78d673470d45 rnalfold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnalfold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,92 @@
+
+ calculates locally stable secondary structures of RNA
+
+
+
+
+ RNALfold
+ macros.xml
+
+
+ $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
+]]>
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diff -r 000000000000 -r 78d673470d45 rnapaln.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnapaln.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,108 @@
+
+ RNA alignment based on sequence base pairing propensities
+
+
+
+
+
+ RNApaln
+ macros.xml
+
+
+ $output
+ --mode=$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
+]]>
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diff -r 000000000000 -r 78d673470d45 rnapdist.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnapdist.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,96 @@
+
+ Calculate distances between thermodynamic RNA secondary structure ensembles
+
+
+
+
+
+ RNApdist
+ macros.xml
+
+
+ $output
+ --compare=$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
+
+]]>
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diff -r 000000000000 -r 78d673470d45 rnapkplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnapkplex.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,89 @@
+
+ predicts RNA secondary structures including pseudoknots
+
+
+
+
+ RNAPKplex
+ macros.xml
+
+
+ $output
+ -T$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
+]]>
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diff -r 000000000000 -r 78d673470d45 rnaplex.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaplex.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,126 @@
+
+ Find targets of a query RNA
+
+
+
+
+ RNAplex
+ macros.xml
+
+
+ $output
+]]>
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diff -r 000000000000 -r 78d673470d45 rnaplfold.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaplfold.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,110 @@
+
+ predicts RNA secondary structures including pseudoknots
+
+
+
+
+ RNAplfold
+ macros.xml
+
+
+ files.tmp
+ ;tar -cf $outputf --files-from=files.tmp
+
+]]>
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diff -r 000000000000 -r 78d673470d45 rnaplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaplot.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,78 @@
+
+ Draw RNA Secondary Structures
+
+
+
+
+ RNAplot
+ macros.xml
+
+
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diff -r 000000000000 -r 78d673470d45 rnasnoop.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnasnoop.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,131 @@
+
+ Find targets of a query H/ACA snoRNA
+
+
+
+
+ RNAsnoop
+ macros.xml
+
+
+ $output
+ --alignmentLenght=$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
+]]>
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+ filetypeOptions['filetypeSelector'] == "fasta"
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+
+' 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.
+
+
+]]>
+
+
+
diff -r 000000000000 -r 78d673470d45 rnasubopt.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnasubopt.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,126 @@
+
+ Calculates suboptimal secondary structures of RNAs
+
+
+
+
+ RNAsubopt
+ macros.xml
+
+
+ $output
+ -T$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
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 78d673470d45 rnaup.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaup.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,117 @@
+
+ Calculate the thermodynamics of RNA-RNA interactions
+
+
+
+
+ RNAup
+ macros.xml
+
+
+ $output
+ -T$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
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 78d673470d45 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Feb 04 12:05:27 2015 -0500
@@ -0,0 +1,6 @@
+
+
+
+
+
+