Mercurial > repos > xuebing > sharplab_seq_motif
diff dreme.xml @ 15:0e221dbd17b2 default tip
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author | xuebing |
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date | Sat, 31 Mar 2012 08:53:06 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dreme.xml Sat Mar 31 08:53:06 2012 -0400 @@ -0,0 +1,50 @@ +<tool id="dreme" name="DREME"> + <description>short motif discovery</description> + <command interpreter="python">/Users/xuebing/bin/dreme.py -p $input -png -e $ethresh + #if $background_select.bg_select == "fromfile": + -n "${bgfile}" + #end if + + && mv dreme_out/dreme.html ${html_outfile} + + && mv dreme_out/dreme.txt ${txt_outfile} + + && mv dreme_out/dreme.xml ${xml_outfile} + + && rm -rf dreme_out + + </command> + <inputs> + <param name="input" type="data" format="fasta" label="Sequence file (FASTA)"/> + <conditional name="background_select"> + <param name="bg_select" type="select" label="Background sequence" > + <option value="shuffle" selected="true">shuffle the orignal sequence</option> + <option value="fromfile">load from file</option> + </param> + <when value="fromfile"> + <param name="bgfile" type="data" format="fasta" label="Background sequence file (FASTA)"/> + </when> + </conditional> + + <param name="ethresh" size="10" type="float" value="0.05" label="E-value threshold"/> + </inputs> + <outputs> + + <data format="xml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/> + <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (motif)"/> + <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/> + </outputs> + <help> + +**What it does** + +http://meme.sdsc.edu/meme/doc/dreme.html + +DREME (Discriminative Regular Expression Motif Elicitation) finds relatively short motifs (up to 8 bases) fast, and can perform discriminative motif discovery if given a negative set, consisting of sequences unlikely to contain a motif of interest that is however likely to be found in the main ("positive") sequence set. If you do not provide a negative set the program shuffles the positive set to provide a background (in the role of the negative set). + +The input to DREME is one or two sets of DNA sequences. The program uses a Fisher Exact Test to determine significance of each motif found in the postive set as compared with its representation in the negative set, using a significance threshold that may be set on the command line. + +DREME achieves its high speed by restricting its search to regular expressions based on the IUPAC alphabet representing bases and ambiguous characters, and by using a heuristic estimate of generalised motifs' statistical significance. + + </help> +</tool>