# HG changeset patch
# User iuc
# Date 1524672788 14400
# Node ID 793225b112029011888d89f02af25b815d49e69f
# Parent a0fa4efeeee33ada1bccd6382820362027a0e8eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dreme1.html Wed Apr 25 12:13:08 2018 -0400
@@ -0,0 +1,6199 @@
+
+
+
+ DREME
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The name of the motif uses the IUPAC codes for nucleotides which has
+ a different letter to represent each of the 15 possible combinations.
+
+
+ The name is itself a representation of the motif though the position
+ weight matrix is not directly equalivant as it is generated from the
+ sites found that matched the letters given in the name.
+
+
+
+ Read more about the MEME suite's use of the IUPAC alphabets.
+
+
+
+
+
+
The logo of the motif.
+
+
+
The logo of the reverse complement motif.
+
+
+
The E-value is the enrichment p-value times the number of candidate
+ motifs tested.
+
The enrichment p-value is calculated using Fisher's Exact Test for
+ enrichment of the motif in the positive sequences.
+
Note that the counts used in Fisher's Exact Test are made after
+ erasing sites that match previously found motifs.
+
+
+
The E-value of the motif calculated without erasing the sites of
+ previously found motifs.
+
+
+
Show more information on the motif.
+
+
+
Submit your motif to another MEME Suite program or download your motif.
+
Supported Programs
+
+ Tomtom
+ Tomtom is a tool for searching for similar known motifs.
+
+ MAST
+ MAST is a tool for searching biological sequence databases for
+ sequences that contain one or more of a group of known motifs.
+
+ FIMO
+ FIMO is a tool for searching biological sequence databases for
+ sequences that contain one or more known motifs.
+
+ GOMO
+ GOMO is a tool for identifying possible roles (Gene Ontology
+ terms) for DNA binding motifs.
+
+ SpaMo
+ SpaMo is a tool for inferring possible transcription factor
+ complexes by finding motifs with enriched spacings.
+
+
+
+
+
# positive sequences matching the motif / # positive sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
# negative sequences matching the motif / # negative sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
The p-value of Fisher's Exact Test for enrichment of the motif in
+ the positive sequences.
+
Note that the counts used in Fisher's Exact Test are made after
+ erasing sites that match previously found motifs.
+
+
+
The E-value is the motif p-value times the number of candidate motifs
+ tested.
+
Note that the p-value was calculated with counts made after
+ erasing sites that match previously found motifs.
+
+
+
The E-value of the motif calculated without erasing the sites of
+ previously found motifs.
+
+
+
All words matching the motif whose uncorrected p-value is less than
+
+
+
+
+
# positive sequences with matches to the word / # positive sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
# negative sequences with matches to the word / # negative sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
The p-value of Fisher's Exact Test for enrichment of the word in
+ the positive sequences.
+
Note that the counts used in Fisher's Exact Test are made after
+ erasing sites that match previously found motifs.
+
+
+
The word p-value times the number of candidates tested.
+
Note that the p-value was calculated with counts made after
+ erasing sites that match previously found motifs.
+
+
+
The sequence file used by DREME to find the motifs.
+
+
+
The alphabet of the sequences.
+
+
+
The count of the sequences.
+
+
+
The name of the alphabet symbol.
+
+
+
The frequency of the alphabet symbol in the control dataset.
+
+
+
+
+
Details
+
+
+
+ Positives
+ Negatives
+ P-value
+ E-value
+ Unerased E-value
+
+
+
+
+
+
+
+
+
+
+
+
Enriched Matching Words
+
+
+
+
+
DREME
+
Discriminative Regular Expression Motif Elicitation
+
+
+ For further information on how to interpret these results or to get a
+ copy of the MEME software please access
+ http://meme.nbcr.net .
+
+
+ If you use DREME in your research please cite the following paper:
+ Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics , 27 (12):1653-1659, 2011.
+ [full text]
+
+
+
Javascript is required to view these results! Your browser does not support canvas!
+
+
+
+
+
+
+
+
No motifs were discovered!
+
+
Sequences
+
+
+
Control Sequences
+
+
+
Background
+
+
+
Other Settings
+
+
+
+
+
+
DREME version
+
+
+
+
Reference
+
+ Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics , 27 (12):1653-1659, 2011.
+ [full text]
+
+
+
+
Command line
+
+
+
+
+
+ dreme -oc dreme_out -rna -norc -p dreme_test_sites.fa -e 0
+
+
+ none
+ 100
+ 0.01
+ 1
+ ThinkPad-T450s
+ Thu Apr 19 19:40:08 CEST 2018
+
+
diff -r a0fa4efeeee3 -r 793225b11202 test-data/dreme2.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dreme2.html Wed Apr 25 12:13:08 2018 -0400
@@ -0,0 +1,6118 @@
+
+
+
+ DREME
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The name of the motif uses the IUPAC codes for nucleotides which has
+ a different letter to represent each of the 15 possible combinations.
+
+
+ The name is itself a representation of the motif though the position
+ weight matrix is not directly equalivant as it is generated from the
+ sites found that matched the letters given in the name.
+
+
+
+ Read more about the MEME suite's use of the IUPAC alphabets.
+
+
+
+
+
+
The logo of the motif.
+
+
+
The logo of the reverse complement motif.
+
+
+
The E-value is the enrichment p-value times the number of candidate
+ motifs tested.
+
The enrichment p-value is calculated using Fisher's Exact Test for
+ enrichment of the motif in the positive sequences.
+
Note that the counts used in Fisher's Exact Test are made after
+ erasing sites that match previously found motifs.
+
+
+
The E-value of the motif calculated without erasing the sites of
+ previously found motifs.
+
+
+
Show more information on the motif.
+
+
+
Submit your motif to another MEME Suite program or download your motif.
+
Supported Programs
+
+ Tomtom
+ Tomtom is a tool for searching for similar known motifs.
+
+ MAST
+ MAST is a tool for searching biological sequence databases for
+ sequences that contain one or more of a group of known motifs.
+
+ FIMO
+ FIMO is a tool for searching biological sequence databases for
+ sequences that contain one or more known motifs.
+
+ GOMO
+ GOMO is a tool for identifying possible roles (Gene Ontology
+ terms) for DNA binding motifs.
+
+ SpaMo
+ SpaMo is a tool for inferring possible transcription factor
+ complexes by finding motifs with enriched spacings.
+
+
+
+
+
# positive sequences matching the motif / # positive sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
# negative sequences matching the motif / # negative sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
The p-value of Fisher's Exact Test for enrichment of the motif in
+ the positive sequences.
+
Note that the counts used in Fisher's Exact Test are made after
+ erasing sites that match previously found motifs.
+
+
+
The E-value is the motif p-value times the number of candidate motifs
+ tested.
+
Note that the p-value was calculated with counts made after
+ erasing sites that match previously found motifs.
+
+
+
The E-value of the motif calculated without erasing the sites of
+ previously found motifs.
+
+
+
All words matching the motif whose uncorrected p-value is less than
+
+
+
+
+
# positive sequences with matches to the word / # positive sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
# negative sequences with matches to the word / # negative sequences.
+
Note these counts are made after erasing sites that match previously
+ found motifs.
+
+
+
The p-value of Fisher's Exact Test for enrichment of the word in
+ the positive sequences.
+
Note that the counts used in Fisher's Exact Test are made after
+ erasing sites that match previously found motifs.
+
+
+
The word p-value times the number of candidates tested.
+
Note that the p-value was calculated with counts made after
+ erasing sites that match previously found motifs.
+
+
+
The sequence file used by DREME to find the motifs.
+
+
+
The alphabet of the sequences.
+
+
+
The count of the sequences.
+
+
+
The name of the alphabet symbol.
+
+
+
The frequency of the alphabet symbol in the control dataset.
+
+
+
+
+
Details
+
+
+
+ Positives
+ Negatives
+ P-value
+ E-value
+ Unerased E-value
+
+
+
+
+
+
+
+
+
+
+
+
Enriched Matching Words
+
+
+
+
+
DREME
+
Discriminative Regular Expression Motif Elicitation
+
+
+ For further information on how to interpret these results or to get a
+ copy of the MEME software please access
+ http://meme.nbcr.net .
+
+
+ If you use DREME in your research please cite the following paper:
+ Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics , 27 (12):1653-1659, 2011.
+ [full text]
+
+
+
Javascript is required to view these results! Your browser does not support canvas!
+
+
+
+
+
+
+
+
No motifs were discovered!
+
+
Sequences
+
+
+
Control Sequences
+
+
+
Background
+
+
+
Other Settings
+
+
+
+
+
+
DREME version
+
+
+
+
Reference
+
+ Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", Bioinformatics , 27 (12):1653-1659, 2011.
+ [full text]
+
+
+
+
Command line
+
+
+
+
+