Mercurial > repos > iuc > meme_meme
diff test-data/dreme_output_test2.html @ 18:19237efe98d1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
| author | iuc |
|---|---|
| date | Sat, 09 Apr 2022 08:34:02 +0000 |
| parents | 3f0dd362b755 |
| children |
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--- a/test-data/dreme_output_test2.html Sat Nov 27 14:38:35 2021 +0000 +++ b/test-data/dreme_output_test2.html Sat Apr 09 08:34:02 2022 +0000 @@ -1,167 +1,50 @@ -<!DOCTYPE HTML> -<html> - <head> - <meta charset="UTF-8"> - <title>DREME</title> - <script> - // @JSON_VAR data - var data = { - "program": "dreme", - "version": "5.0.5", - "release": "Mon Mar 18 20:12:19 2019 -0700", - "cmd": [ - "dreme", "-o", "./dreme_out", "-p", - "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink", - "4", "-maxk", "10" - ], - "options": { - "revcomp": false, - "ngen": 100, - "add_pv_thresh": 0.01, - "seed": 1, - "stop": { - "evalue": "1e-05" - } - }, - "alphabet": { - "name": "RNA", - "like": "rna", - "ncore": 4, - "symbols": [ - { - "symbol": "A", - "name": "Adenine", - "colour": "CC0000" - }, { - "symbol": "C", - "name": "Cytosine", - "colour": "0000CC" - "symbol": "G", - "name": "Guanine", - "colour": "FFB300" - "symbol": "U", - "aliases": "T", - "name": "Uracil", - "colour": "008000" - "symbol": "N", - "aliases": "X.", - "name": "Any base", - "equals": "ACGU" - "symbol": "V", - "name": "Not U", - "equals": "ACG" - "symbol": "H", - "name": "Not G", - "equals": "ACU" - "symbol": "D", - "name": "Not C", - "equals": "AGU" - "symbol": "B", - "name": "Not A", - "equals": "CGU" - "symbol": "M", - "name": "Amino", - "equals": "AC" - "symbol": "R", - "name": "Purine", - "equals": "AG" - "symbol": "W", - "name": "Weak", - "equals": "AU" - "symbol": "S", - "name": "Strong", - "equals": "CG" - "symbol": "Y", - "name": "Pyrimidine", - "equals": "CU" - "symbol": "K", - "name": "Keto", - "equals": "GU" - "background": { - "freqs": [0.221, 0.245, 0.221, 0.312] - "sequence_db": { - "count": 1000 - "control_db": { - "name": "shuffled positive sequences", - "from": "shuffled", - "count": 1000, - "freqs": [0.221, 0.245, 0.221, 0.312] - "motifs": [ - "db": 0, - "id": "UUYUCY", - "alt": "DREME-1", - "len": 6, - "nsites": 459, - "evalue": "3.3e-013", - "p": 387, - "n": 210, - "pvalue": "2.6e-018", - "unerased_evalue": "3.3e-013", - "pwm": [ - [0.000000, 0.000000, 0.000000, 1.000000], - [0.000000, 0.000000, 0.000000, 1.000000], - [0.000000, 0.294118, 0.000000, 0.705882], - [0.000000, 0.000000, 0.000000, 1.000000], - [0.000000, 1.000000, 0.000000, 0.000000], - [0.000000, 0.474946, 0.000000, 0.525054] - "matches": [ - "seq": "UUUUCC", - "p": 147, - "n": 75, - "pvalue": "1.8e-007", - "evalue": "2.2e-002" - </script> -var site_url = "http://meme-suite.org"; -//====================================================================== -// end RasterizedAlphabet -//====================================================================== -//====================================================================== -// start LogoMetrics object -//====================================================================== - * Initialise and display the download popup. -</style> - </head> - <body data-scrollpad="true"> - <!-- --> - <div id="grey_out_page" class="grey_background" style="display:none;"> - The name of the motif uses the IUPAC codes for nucleotides which has - a different letter to represent each of the 15 possible combinations. - The name is itself a representation of the motif though the position - weight matrix is not directly equivalent as it is generated from the - sites found that matched the letters given in the name. - <p>The logo of the motif.</p> - <p>The logo of the reverse complement motif.</p> - <p>The E-value is the enrichment p-value times the number of candidate - motifs tested.</p> - <p>The enrichment p-value is calculated using Fisher's Exact Test for - enrichment of the motif in the positive sequences.</p> - <p>Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.</p> - <p>The E-value of the motif calculated without erasing the sites of - previously found motifs.</p> - <p>Show more information on the motif.</p> - <p>Submit your motif to another MEME Suite program or download your motif.</p> - <h5>Supported Programs</h5> - <dt>Tomtom</dt> - <dd>Tomtom is a tool for searching for similar known motifs. - <dt>MAST</dt> - <dd>MAST is a tool for searching biological sequence databases for - sequences that contain one or more of a group of known motifs. - <dt>FIMO</dt> - <dd>FIMO is a tool for searching biological sequence databases for - sequences that contain one or more known motifs. - <dt>GOMo</dt> - <dd>GOMo is a tool for identifying possible roles (Gene Ontology - terms) for DNA binding motifs. - <dt>SpaMo</dt> - <dd>SpaMo is a tool for inferring possible transcription factor - complexes by finding motifs with enriched spacings. - <!-- Page starts here --> - <h1>DREME</h1> - <h2>Discriminative Regular Expression Motif Elicitation</h2> - For further information on how to interpret these results please access - To get a copy of the MEME software please access - If you use DREME in your research please cite the following paper:<br /> - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011. + <h4>Other Settings</h4> + <table id="tbl_settings" class="inputs hide_advanced"> + <tr> + <th>Strand Handling</th> + <td id="opt_strand"> + <span class="strand_none">This alphabet only has one strand</span> + <span class="strand_given">Only the given strand is processed</span> + <span class="strand_both">Both the given and reverse complement strands are processed</span> + </td> + </tr> + <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr> + <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr> + <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr> + <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr> + <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr> + </table> + <script> + { + $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none"); + $("opt_ngen").innerHTML = data.options.ngen; + $("opt_seed").innerHTML = data.options.seed; + $("opt_stop_evalue").innerHTML = data.options.stop.evalue; + $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count."); + $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time."); + } + </script> + </div> + <!-- list information on this program --> + <div id="info_sec" class="bar" style="position:relative"> + <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div> + <div class="subsection"> + <h5 id="version">DREME version</h5> + <span id="ins_version"></span> + (Release date: <span id="ins_release"></span>)<br> + </div> + <script> + $("ins_version").innerHTML = data["version"]; + $("ins_release").innerHTML = data["release"]; + </script> + <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div> + <div class="subsection"> + <h5 id="command">Command line</h5> + <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly"> + </textarea> + <script>$("cmd").value = data["cmd"].join(" ");</script> + </div> + </div> + </body> </html>