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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:05:35 -0500
parents 4eb02864e5df
children c5209f38700d
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--- a/test-data/fimo_output_test2.html	Wed Dec 12 02:50:48 2018 -0500
+++ b/test-data/fimo_output_test2.html	Wed Dec 11 18:05:35 2019 -0500
@@ -9,7 +9,7 @@
 td.right {text-align: right; padding-right: 1cm;}
 </style>
 </head>
-<body bgcolor="#D5F0FF">
+<body color="#000000">
 <a name="top_buttons"></a>
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@@ -17,123 +17,44 @@
 <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>
 </table>
-<br/>
-<br/>
-<hr/>
 <center><big><b>FIMO - Motif search tool</b></big></center>
-<hr>
-<p>
-FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)
-</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>
+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.
-<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 hsa_chrM.fa
-  <br />
   Database contains 1 sequences, 16569 residues
-</p>
-<p>
-  MOTIFS dreme_fimo_input_1.xml (DNA)
   <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>
-      <tr>
-        <td style="text-align:right;">YTAACA</td>
-        <td style="text-align:right;padding-left: 1em;">6</td>
-        <td style="text-align:left;padding-left: 1em;">TTAACA</td>
-       </tr>
-      <tr>
-        <td style="text-align:right;">TCTGT</td>
-        <td style="text-align:right;padding-left: 1em;">5</td>
-        <td style="text-align:left;padding-left: 1em;">TCTGT</td>
-       </tr>
-      <tr>
-        <td style="text-align:right;">SCCAGG</td>
-        <td style="text-align:right;padding-left: 1em;">6</td>
-        <td style="text-align:left;padding-left: 1em;">CCCAGG</td>
-       </tr>
-      <tr>
-        <td style="text-align:right;">CCAGCAY</td>
-        <td style="text-align:right;padding-left: 1em;">7</td>
-        <td style="text-align:left;padding-left: 1em;">CCAGCAC</td>
-       </tr>
-      <tr>
-        <td style="text-align:right;">GMATGT</td>
-        <td style="text-align:right;padding-left: 1em;">6</td>
-        <td style="text-align:left;padding-left: 1em;">GAATGT</td>
-       </tr>
     </tbody>
   </table>
-</p>
-<p>
-Random model letter frequencies (fimo_background_probs_hsa_chrM.txt):
-<br/>
-
 A 0.278 C 0.222 G 0.222 T 0.278 </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 11 motif occurences with a p-value less than 0.0001.
-
 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> 
+TSV (tab-delimited values) output file
+the GFF3 file 
 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
+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.
-</li>
-<li>
 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.
-</li>
-<li>
 The q-value of a motif occurrence is defined as the
 false discovery rate if the occurrence is accepted as significant.
-</li>
-<li>The table is sorted by increasing p-value.</li>
-</ul>
-<table border="1">
-<thead>
-<tr>
+<li>The table is sorted by increasing <i>p</i>-value.</li>
 <th>Motif ID</th>
 <th>Alt ID</th>
 <th>Sequence Name</th>
@@ -143,9 +64,6 @@
 <th>p-value</th>
 <th>q-value</th>
 <th>Matched Sequence</th>
-</tr>
-</thead>
-<tbody>
     <tr>
       <td style="text-align:left;">CCAGCAY</td>
       <td style="text-align:left;">DREME-5</td>
@@ -154,172 +72,19 @@
       <td style="text-align:left;">510</td>
       <td style="text-align:left;">516</td>
       <td style="text-align:left;">4.15e-05</td>
-      <td style="text-align:left;">0.668</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
-   </tr>
-    <tr>
-      <td style="text-align:left;">CCAGCAY</td>
-      <td style="text-align:left;">DREME-5</td>
-      <td style="text-align:left;">chrM</td>
-      <td style="text-align:center;">+</td>
-      <td style="text-align:left;">5137</td>
-      <td style="text-align:left;">5143</td>
-      <td style="text-align:left;">4.15e-05</td>
-      <td style="text-align:left;">0.668</td>
+      <td style="text-align:left;">0.683</td>
       <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
-   </tr>
-    <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;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <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;">2093</td>
       <td style="text-align:left;">2099</td>
       <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <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;">2299</td>
-      <td style="text-align:left;">2305</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <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;">5186</td>
-      <td style="text-align:left;">5192</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <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;">6530</td>
-      <td style="text-align:left;">6536</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <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;">7742</td>
-      <td style="text-align:left;">7748</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <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;">13657</td>
-      <td style="text-align:left;">13663</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;">0.332</td>
       <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
    </tr>
-    <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;">13741</td>
-      <td style="text-align:left;">13747</td>
-      <td style="text-align:left;">8.2e-05</td>
-      <td style="text-align:left;">0.327</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
-   </tr>
-    <tr>
-      <td style="text-align:left;">CCAGCAY</td>
-      <td style="text-align:left;">DREME-5</td>
-      <td style="text-align:left;">chrM</td>
-      <td style="text-align:center;">+</td>
-      <td style="text-align:left;">4241</td>
-      <td style="text-align:left;">4247</td>
-      <td style="text-align:left;">9.37e-05</td>
-      <td style="text-align:left;">1</td>
-      <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAT</td>
-   </tr>
-</tbody>
-</table>
-
 <hr>
 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
-<hr>
-<p>
 Command line:
-</p>
-<pre>
-fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa
-</pre>
-<p>
 Settings:
-</p>
-<pre>
-<table>
-  <tr>
-    <td style="padding-right: 2em">output_directory = fimo_test2_out</td>
-    <td style="padding-left: 5em; padding-right: 2em">MEME file name = dreme_fimo_input_1.xml</td>
-    <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>
-  </tr>  <tr>
-    <td style="padding-right: 2em">background file name = fimo_background_probs_hsa_chrM.txt</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 = true</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>
-</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>
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