Mercurial > repos > xuebing > sharplab_seq_motif
comparison mytools/dreme.xml @ 0:39217fa39ff2
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| author | xuebing |
|---|---|
| date | Tue, 13 Mar 2012 23:34:52 -0400 |
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| -1:000000000000 | 0:39217fa39ff2 |
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| 1 <tool id="dreme" name="DREME"> | |
| 2 <description>short motif discovery</description> | |
| 3 <command interpreter="python">/Users/xuebing/bin/dreme.py -p $input -png -e $ethresh | |
| 4 #if $background_select.bg_select == "fromfile": | |
| 5 -n "${bgfile}" | |
| 6 #end if | |
| 7 | |
| 8 && mv dreme_out/dreme.html ${html_outfile} | |
| 9 | |
| 10 && mv dreme_out/dreme.txt ${txt_outfile} | |
| 11 | |
| 12 && mv dreme_out/dreme.xml ${xml_outfile} | |
| 13 | |
| 14 && rm -rf dreme_out | |
| 15 | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input" type="data" format="fasta" label="Sequence file (FASTA)"/> | |
| 19 <conditional name="background_select"> | |
| 20 <param name="bg_select" type="select" label="Background sequence" > | |
| 21 <option value="shuffle" selected="true">shuffle the orignal sequence</option> | |
| 22 <option value="fromfile">load from file</option> | |
| 23 </param> | |
| 24 <when value="fromfile"> | |
| 25 <param name="bgfile" type="data" format="fasta" label="Background sequence file (FASTA)"/> | |
| 26 </when> | |
| 27 </conditional> | |
| 28 | |
| 29 <param name="ethresh" size="10" type="float" value="0.05" label="E-value threshold"/> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 | |
| 33 <data format="xml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/> | |
| 34 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (motif)"/> | |
| 35 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/> | |
| 36 </outputs> | |
| 37 <help> | |
| 38 | |
| 39 **What it does** | |
| 40 | |
| 41 http://meme.sdsc.edu/meme/doc/dreme.html | |
| 42 | |
| 43 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). | |
| 44 | |
| 45 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. | |
| 46 | |
| 47 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. | |
| 48 | |
| 49 </help> | |
| 50 </tool> |