Mercurial > repos > iuc > meme_fimo
diff test-data/fimo_output_test3.html @ 18:c5209f38700d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
| author | iuc |
|---|---|
| date | Sat, 09 Apr 2022 08:32:23 +0000 |
| parents | 0c5239d1aa65 |
| children |
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--- a/test-data/fimo_output_test3.html Sat Nov 27 14:37:42 2021 +0000 +++ b/test-data/fimo_output_test3.html Sat Apr 09 08:32:23 2022 +0000 @@ -1,92 +1,23 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> -<meta charset="UTF-8"> -<title>FIMO Results</title> -<style type="text/css"> -</head> -<body color="#000000"> -<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> -<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td> -<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> -<td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td> -<td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td> -<center><big><b>FIMO - Motif search tool</b></big></center> -FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700) -For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br> -To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a> -<p>If you use FIMO in your research, please cite the following paper:<br> -Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, -"FIMO: Scanning for occurrences of a given motif", -<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. -<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center> - Database contains 1 sequences, 16569 residues - <table> - <thead> - <tr> - <th style="border-bottom: 1px dashed;">MOTIF</th> - <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th> - <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" > - BEST POSSIBLE MATCH - </th> - </tr> - </thead> - <tbody> - <tr> - <td style="text-align:right;">ACTAAYH</td> - <td style="text-align:right;padding-left: 1em;">7</td> - <td style="text-align:left;padding-left: 1em;">ACTAACA</td> - </tr> - </tbody> - </table> -</p> -<p> -Random model letter frequencies (--uniform--): -A 0.250 C 0.250 G 0.250 T 0.250 </p> -<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center> -There were 517 motif occurences with a p-value less than 0.01. -The full set of motif occurences can be seen in the -TSV (tab-delimited values) output file -the GFF3 file -which may be suitable for uploading to the -(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), -or the XML file -The <i>p</i>-value of a motif occurrence is defined as the -probability of a random sequence of the same length as the motif -matching that position of the sequence with as good or better a score. -The score for the match of a position in a sequence to a motif -is computed by summing the appropriate entries from each column of -the position-dependent scoring matrix that represents the motif. -The q-value of a motif occurrence is defined as the -false discovery rate if the occurrence is accepted as significant. -<li>The table is sorted by increasing <i>p</i>-value.</li> -<table border="1"> -<thead> -<tr> -<th>Motif ID</th> -<th>Alt ID</th> -<th>Sequence Name</th> -<th>Strand</th> -<th>Start</th> -<th>End</th> -<th>p-value</th> -<th>q-value</th> -<th>Matched Sequence</th> -</tr> -</thead> -<tbody> - <tr> - <td style="text-align:left;">ACTAAYH</td> - <td style="text-align:left;">DREME-1</td> - <td style="text-align:left;">chrM</td> - <td style="text-align:center;">+</td> - <td style="text-align:left;">440</td> - <td style="text-align:left;">446</td> - <td style="text-align:left;">6.1e-05</td> - <td style="text-align:left;">0.239</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td> -This information can be useful in the event you wish to report a -problem with the FIMO software. -</body> -</html> + <td style="padding-right: 2em">background file name = --uniform--</td> + <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td> + <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td> + </tr> <tr> + <td style="padding-right: 2em">allow clobber = false</td> + <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td> + <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td> + </tr> + <tr> + <td style="padding-right: 2em">text only = false</td> + <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td> + <td style="padding-left: 5em; padding-right: 2em">max strand = false</td> + </tr> + <tr> + <td style="padding-right: 2em">threshold type = p-value</td> + <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.01</td> + <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td> + </tr> + <tr> + <td style="padding-right: 2em">alpha = 1</td> + <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td> + <td style="padding-left: 5em; padding-right: 2em"></td> + </tr> \ No newline at end of file