Mercurial > repos > iuc > meme_dreme
diff test-data/dreme_output_test1.html @ 5:f33d77dcacce draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
| author | iuc |
|---|---|
| date | Sat, 09 Apr 2022 08:32:58 +0000 |
| parents | 3e5c80594237 |
| children |
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--- a/test-data/dreme_output_test1.html Sat Nov 27 14:39:01 2021 +0000 +++ b/test-data/dreme_output_test1.html Sat Apr 09 08:32:58 2022 +0000 @@ -1,113 +1,100 @@ -<!DOCTYPE HTML> -<html> - <head> - <meta charset="UTF-8"> - <title>DREME</title> - <script> - // @JSON_VAR data - var data = { - "program": "dreme", - "version": "5.0.5", - "cmd": [ - "dreme", "-o", "./dreme_out", "-p", - "-norc", "-rna", "-s", "1" - ], - "options": { - "revcomp": false, - "ngen": 100, - "add_pv_thresh": 0.01, - "seed": 1, - "stop": { - "evalue": "0.05" - "alphabet": { - "name": "RNA", - "like": "rna", - "ncore": 4, - "symbols": [ - "background": { - "freqs": [0.221, 0.245, 0.221, 0.312] - "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": "1.2e-013", - "p": 387, - "n": 210, - "pvalue": "2.6e-018", - "unerased_evalue": "1.2e-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": "8.1e-003" - }, { - "seq": "UUUUCU", - "p": 155, - "n": 94, - "pvalue": "2.2e-005", - "evalue": "1.0e+000" - "seq": "UUCUCU", - "p": 94, - "n": 51, - "pvalue": "1.3e-004", - "evalue": "6.1e+000" - "seq": "UUCUCC", - "p": 75, - "n": 42, - "pvalue": "1.1e-003", - "evalue": "5.0e+001" - <script> -var site_url = "http://meme-suite.org"; -</script> -/* dreme output specific css */ -/* program settings */ -</style> - </head> - <body data-scrollpad="true"> - 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 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. + </div> + <div class="box"> + <h4>Sequences</h4> + <table id="seq_info" class="inputs"> + <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th> + <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th> + <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th> + </tr> + <tr> + <td id="ins_seq_source"></td> + <td id="ins_seq_alphabet"></td> + <td id="ins_seq_count"></td> + </tr> + </table> + <script> + { + var db = data.sequence_db; + $("ins_seq_source").innerHTML = db.file; + $("ins_seq_alphabet").innerHTML = current_alphabet.get_alphabet_name(); + $("ins_seq_count").innerHTML = db.count; + } + </script> + <h4>Control Sequences</h4> + <table id="seq_info" class="inputs"> + <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th> + <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th> + </tr> + <tr> + <td id="ins_cseq_source"></td> + <td id="ins_cseq_count"></td> + </tr> + </table> + <script> + { + var db = data.control_db; + if (db.from == "shuffled") { + $("ins_cseq_source").innerHTML = "Shuffled Sequences"; + } else { + $("ins_cseq_source").innerHTML = db.file; + } + $("ins_cseq_count").innerHTML = db.count; + } + </script> + <h4>Background</h4> + <span id="alpha_bg"></span> + <script> + { + $("alpha_bg").appendChild(make_alpha_bg_table(current_alphabet, data.control_db.freqs)); + } + </script> + <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>