Mercurial > repos > xuebing > sharplabtool
diff dreme.xml @ 14:76e1b1b21cce default tip
Deleted selected files
author | xuebing |
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date | Tue, 13 Mar 2012 19:05:10 -0400 |
parents | 292186c14b08 |
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--- a/dreme.xml Sat Mar 10 08:17:36 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -<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>