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