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diff test-data/fimo_output_test1.html @ 5:f33d77dcacce draft default tip

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"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/fimo_output_test1.html	Sat Nov 27 14:39:01 2021 +0000
+++ b/test-data/fimo_output_test1.html	Sat Apr 09 08:32:58 2022 +0000
@@ -1,73 +1,34 @@
-<!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;}
-</head>
-<body color="#000000">
-<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>
-<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>
-</tr>
+    <td style="padding-right: 2em">background file name = --nrdb--</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 = 0.0001</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>
+
 </table>
-<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
-         BEST POSSIBLE MATCH
-Random model letter frequencies (--nrdb--):
-A 0.275 C 0.225 G 0.225 T 0.275 </p>
-<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
-There were 11 motif occurences with a p-value less than 0.0001.
-The full set of motif occurences can be seen in the
-TSV (tab-delimited values) output 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>
-<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>
-      <td style="text-align:left;">TACTAAYM</td>
-      <td style="text-align:left;">MEME-1</td>
-      <td style="text-align:left;">chrM</td>
-      <td style="text-align:center;">+</td>
-      <td style="text-align:left;">6529</td>
-      <td style="text-align:left;">6536</td>
-      <td style="text-align:left;">2.18e-05</td>
-      <td style="text-align:left;">0.142</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td>
-</table>
-<hr>
-<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
+</pre>
+<p>
 This information can be useful in the event you wish to report a
 problem with the FIMO software.
+</p>
+<hr>
+<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
 </body>
 </html>