Mercurial > repos > hogart > unafold
changeset 0:e186a2d22ea0 draft
Uploaded unafold.xml
| author | hogart |
|---|---|
| date | Tue, 10 Mar 2015 05:43:46 -0400 |
| parents | |
| children | 51baa0ab6def |
| files | unafold.xml |
| diffstat | 1 files changed, 747 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/unafold.xml Tue Mar 10 05:43:46 2015 -0400 @@ -0,0 +1,747 @@ + + + +<!DOCTYPE html> +<html lang="en" class=""> + <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#"> + <meta charset='utf-8'> + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta http-equiv="Content-Language" content="en"> + + + <title>galaxy-tools-unafold/unafold.xml at master · DrHogart/galaxy-tools-unafold · GitHub</title> + <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> + <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> + <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> + <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> + <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> + <link 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+ + + <a class="octicon-button disabled tooltipped tooltipped-w" href="#" + aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a> + + <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#" + aria-label="You must be signed in to make or propose changes"> + </a> + </div><!-- /.actions --> + <div class="file-info"> + 58 lines (41 sloc) + <span class="file-info-divider"></span> + 2.602 kb + </div> + </div> + + <div class="blob-wrapper data type-xml"> + <table class="highlight tab-size-8 js-file-line-container"> + <tr> + <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> + <td id="LC1" class="blob-code js-file-line"><?<span class="pl-ent">xml</span><span class="pl-e"> version</span>=<span class="pl-s1"><span class="pl-pds">"</span>1.0<span class="pl-pds">"</span></span>?></td> + </tr> + <tr> + <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> + <td id="LC2" class="blob-code js-file-line"><<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold_1<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s1"><span class="pl-pds">"</span>0.0.1<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> + <td id="LC3" class="blob-code js-file-line"> <<span class="pl-ent">description</span>>Folding of RNA sequences using UNAFold</<span class="pl-ent">description</span>></td> + </tr> + <tr> + <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> + <td id="LC4" class="blob-code js-file-line"> <<span class="pl-ent">command</span> <span class="pl-e">interpreter</span>=<span class="pl-s1"><span class="pl-pds">"</span>bash<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> + <td id="LC5" class="blob-code js-file-line">unafold.sh -i $inputFastaFile -o $outputArhive -t '$outputArhive.extra_files_path' -a ${ na_type.nucacid } -c $tmp</td> + </tr> + <tr> + <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> + <td id="LC6" class="blob-code js-file-line">#if str($na_type.nucacid) == 'dna':</td> + </tr> + <tr> + <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> + <td id="LC7" class="blob-code js-file-line"> -s ${ na_type.sodium } -m ${ na_type.magnesium }</td> + </tr> + <tr> + <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> + <td id="LC8" class="blob-code js-file-line">#end if</td> + </tr> + <tr> + <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> + <td id="LC9" class="blob-code js-file-line"> > $outputLog</td> + </tr> + <tr> + <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> + <td id="LC10" class="blob-code js-file-line"> </<span class="pl-ent">command</span>></td> + </tr> + <tr> + <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> + <td id="LC11" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> + <td id="LC12" class="blob-code js-file-line"> <<span class="pl-ent">inputs</span>></td> + </tr> + <tr> + <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> + <td id="LC13" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">format</span>=<span class="pl-s1"><span class="pl-pds">"</span>fasta<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>inputFastaFile<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>data<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Fasta input file<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> + <td id="LC14" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> + <td id="LC15" class="blob-code js-file-line"> <<span class="pl-ent">conditional</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>na_type<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> + <td id="LC16" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>nucacid<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Nucleic Acid Type<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> + <td id="LC17" class="blob-code js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>rna<span class="pl-pds">"</span></span> <span class="pl-e">selected</span>=<span class="pl-s1"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>>RNA</<span class="pl-ent">option</span>></td> + </tr> + <tr> + <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> + <td id="LC18" class="blob-code js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>dna<span class="pl-pds">"</span></span>>DNA</<span class="pl-ent">option</span>></td> + </tr> + <tr> + <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> + <td id="LC19" class="blob-code js-file-line"> </<span class="pl-ent">param</span>></td> + </tr> + <tr> + <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> + <td id="LC20" class="blob-code js-file-line"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>dna<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> + <td id="LC21" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>sodium<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>float<span class="pl-pds">"</span></span> <span class="pl-e">size</span>=<span class="pl-s1"><span class="pl-pds">"</span>6<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>1.0<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s1"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s1"><span class="pl-pds">"</span>100<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>[Na+] in M<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> + <td id="LC22" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>magnesium<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>float<span class="pl-pds">"</span></span> <span class="pl-e">size</span>=<span class="pl-s1"><span class="pl-pds">"</span>6<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>0.0<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s1"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s1"><span class="pl-pds">"</span>100<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>[Mg++] in M<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> + <td id="LC23" class="blob-code js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> + <td id="LC24" class="blob-code js-file-line"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>rna<span class="pl-pds">"</span></span>></td> + </tr> + <tr> + <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> + <td id="LC25" class="blob-code js-file-line"> <span class="pl-c"><!-- do nothing here --></span></td> + </tr> + <tr> + <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> + <td id="LC26" class="blob-code js-file-line"> </<span class="pl-ent">when</span>></td> + </tr> + <tr> + <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> + <td id="LC27" class="blob-code js-file-line"> </<span class="pl-ent">conditional</span>></td> + </tr> + <tr> + <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> + <td id="LC28" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> + <td id="LC29" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>tmp<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">size</span>=<span class="pl-s1"><span class="pl-pds">"</span>3<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>37<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s1"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s1"><span class="pl-pds">"</span>100<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Temperature (C)<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> + <td id="LC30" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> + <td id="LC31" class="blob-code js-file-line"> </<span class="pl-ent">inputs</span>></td> + </tr> + <tr> + <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> + <td id="LC32" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> + <td id="LC33" class="blob-code js-file-line"> <<span class="pl-ent">outputs</span>></td> + </tr> + <tr> + <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> + <td id="LC34" class="blob-code js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s1"><span class="pl-pds">"</span>zip<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>outputArhive<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Arhive: UNAFold on $on_string<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> + <td id="LC35" class="blob-code js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s1"><span class="pl-pds">"</span>txt<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>outputLog<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Log: UNAFold on $on_string<span class="pl-pds">"</span></span>/></td> + </tr> + <tr> + <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> + <td id="LC36" class="blob-code js-file-line"> </<span class="pl-ent">outputs</span>></td> + </tr> + <tr> + <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> + <td id="LC37" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> + <td id="LC38" class="blob-code js-file-line"><<span class="pl-ent">help</span>></td> + </tr> + <tr> + <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> + <td id="LC39" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> + <td id="LC40" class="blob-code js-file-line">This tool computes the fold of RNA/DNA using UNAFold v.3.8.</td> + </tr> + <tr> + <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> + <td id="LC41" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> + <td id="LC42" class="blob-code js-file-line">UNAFold (http://mfold.rna.albany.edu/?q=unafold-man-pages) is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software.</td> + </tr> + <tr> + <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> + <td id="LC43" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> + <td id="LC44" class="blob-code js-file-line">For melting simulations, the package computes not just melting temperatures, but entire melting profiles. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. ITC (Isothermal Titration Calorimetry) and van't Hoff plots are also simulated.</td> + </tr> + <tr> + <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> + <td id="LC45" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> + <td id="LC46" class="blob-code js-file-line">UNAFold v.3.8 (http://mfold.rna.albany.edu/?q=unafold-man-pages)</td> + </tr> + <tr> + <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> + <td id="LC47" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> + <td id="LC48" class="blob-code js-file-line">Galaxy wrapper for UNAFold v. 0.0.1</td> + </tr> + <tr> + <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> + <td id="LC49" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> + <td id="LC50" class="blob-code js-file-line">Author: Sergei Ryazansky, s.ryazansky@gmail.com</td> + </tr> + <tr> + <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> + <td id="LC51" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> + <td id="LC52" class="blob-code js-file-line">Web-site: https://github.com/DrHogart/galaxy-tools-unafold)</td> + </tr> + <tr> + <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> + <td id="LC53" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> + <td id="LC54" class="blob-code js-file-line"> +</td> + </tr> + <tr> + <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> + <td id="LC55" class="blob-code js-file-line"></<span class="pl-ent">help</span>></td> + </tr> + <tr> + <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> + <td id="LC56" class="blob-code js-file-line"></<span class="pl-ent">tool</span>></td> + </tr> + <tr> + <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> + <td id="LC57" class="blob-code js-file-line"> +</td> + </tr> +</table> + + </div> + +</div> + +<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> +<div id="jump-to-line" style="display:none"> + <form accept-charset="UTF-8" class="js-jump-to-line-form"> + <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> + <button type="submit" class="button">Go</button> + </form> +</div> + + </div> + + </div><!-- /.repo-container --> + <div class="modal-backdrop"></div> + </div><!-- /.container --> + </div><!-- /.site --> + + + </div><!-- /.wrapper --> + + <div class="container"> + <div class="site-footer" role="contentinfo"> + <ul class="site-footer-links right"> + <li><a href="https://status.github.com/" 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