Mercurial > repos > iuc > meme_psp_gen
diff test-data/fimo_output_test1.html @ 3:ff2f53a32d0e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2019 18:04:34 -0500 |
| parents | b48e673af4e8 |
| children | 5f95d385a33c |
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--- a/test-data/fimo_output_test1.html Thu May 17 14:11:15 2018 -0400 +++ b/test-data/fimo_output_test1.html Wed Dec 11 18:04:34 2019 -0500 @@ -7,9 +7,8 @@ <style type="text/css"> td.left {text-align: left;} td.right {text-align: right; padding-right: 1cm;} -</style> </head> -<body bgcolor="#D5F0FF"> +<body color="#000000"> <a name="top_buttons"></a> <hr> <table summary="buttons" align="left" cellspacing="0"> @@ -17,98 +16,36 @@ <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 meme_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;">TACTAAYM</td> - <td style="text-align:right;padding-left: 1em;">8</td> - <td style="text-align:left;padding-left: 1em;">TACTAACA</td> - </tr> - </tbody> - </table> -</p> -<p> Random model letter frequencies (--nrdb--): -<br/> - A 0.275 C 0.225 G 0.225 T 0.275 </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> -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 +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. -</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> @@ -118,21 +55,6 @@ <th>p-value</th> <th>q-value</th> <th>Matched Sequence</th> -</tr> -</thead> -<tbody> - <tr> - <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;">2299</td> - <td style="text-align:left;">2306</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> - </tr> - <tr> <td style="text-align:left;">TACTAAYM</td> <td style="text-align:left;">MEME-1</td> <td style="text-align:left;">chrM</td> @@ -142,159 +64,10 @@ <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> - </tr> - <tr> - <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;">7741</td> - <td style="text-align:left;">7748</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> - </tr> - <tr> - <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;">13656</td> - <td style="text-align:left;">13663</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> - </tr> - <tr> - <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;">13740</td> - <td style="text-align:left;">13747</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> - </tr> - <tr> - <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;">861</td> - <td style="text-align:left;">868</td> - <td style="text-align:left;">3.96e-05</td> - <td style="text-align:left;">0.185</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td> - </tr> - <tr> - <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;">9346</td> - <td style="text-align:left;">9353</td> - <td style="text-align:left;">3.96e-05</td> - <td style="text-align:left;">0.185</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td> - </tr> - <tr> - <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;">3767</td> - <td style="text-align:left;">3774</td> - <td style="text-align:left;">6.62e-05</td> - <td style="text-align:left;">0.216</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td> - </tr> - <tr> - <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;">5497</td> - <td style="text-align:left;">5504</td> - <td style="text-align:left;">6.62e-05</td> - <td style="text-align:left;">0.216</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td> - </tr> - <tr> - <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;">10105</td> - <td style="text-align:left;">10112</td> - <td style="text-align:left;">6.62e-05</td> - <td style="text-align:left;">0.216</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td> - </tr> - <tr> - <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;">10959</td> - <td style="text-align:left;">10966</td> - <td style="text-align:left;">8.79e-05</td> - <td style="text-align:left;">0.261</td> - <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACT</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_test1_out meme_fimo_input_1.xml hsa_chrM.fa -</pre> -<p> -Settings: -</p> -<pre> -<table> - <tr> - <td style="padding-right: 2em">output_directory = fimo_test1_out</td> - <td style="padding-left: 5em; padding-right: 2em">MEME file name = meme_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 = --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 = 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> </body> </html>