Mercurial > repos > iuc > meme_meme

diff test-data/fimo_output_html_1.html @ 1:d20e391eb22f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
author: iuc
date: Tue, 22 Dec 2015 17:02:11 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_html_1.html	Tue Dec 22 17:02:11 2015 -0500
@@ -0,0 +1,100 @@
+<!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">
+td.left {text-align: left;}
+td.right {text-align: right; padding-right: 1cm;}
+</style>
+</head>
+<body bgcolor="#D5F0FF">
+<a name="top_buttons"></a>
+<hr>
+<table summary="buttons" align="left" cellspacing="0">
+<tr>
+<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>
+</tr>
+</table>
+<br/>
+<br/>
+<hr/>
+<center><big><b>FIMO - Motif search tool</b></big></center>
+<hr>
+<p>
+FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
+</p>
+<p>
+For further information on how to interpret these results
+or to get a copy of the FIMO software please access
+<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
+<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.
+<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>
+<hr>
+<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
+<hr>
+<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
+<p>
+  DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
+  <br />
+  Database contains 1 sequences, 5386 residues
+</p>
+<p>
+  MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
+  <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;">1</td>
+        <td style="text-align:right;padding-left: 1em;">11</td>
+        <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
+       </tr>
+    </tbody>
+  </table>
+</p>
+<p>
+Random model letter frequencies (from non-redundant database):
+<br/>
+
+A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 
+L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 
+W 0.013 Y 0.033 </p>
+</div>
+<hr>
+<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
+<hr>
+<ul>
+<li>
+There were 1937 motif occurences with a p-value less than 0.0001.
+<b>Only the most significant 1000 matches are shown here.</b>
+
+The full set of motif occurences can be seen in the
+tab-delimited plain text output file
+<a href="fimo.txt">fimo.txt</a>, 
+the GFF file 
+<a href="fimo.gff">fimo.gff</a> 
+which may be suitable for uploading to the 
+<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
+(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
+or the XML file 
+<a href="fimo.xml">fimo.xml</a>.
+</li>
+<li>
+The p-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.
+</li>