view mytools/iupac2meme.xml @ 5:84e2c77a6abd

Uploaded

<tool id="iupac2meme" name="create-motif-file">
  <description>from one sequence</description>
  <command>iupac2meme 
    #if $background_select.bg_select == "fromfile":
    -bg $bgfile
    #end if
  -numseqs $numseqs $logodds $motif > $output </command>
  <inputs>
      <param name="motif" size="20" type="text" value="AATAAA" label="motif sequence" help="IUPAC motif, such as ACGGWNYCGT"/>
      <conditional name="background_select">
    	<param name="bg_select" type="select" label="Background model" >
		  <option value="uniform" selected="true">uniform</option>
		  <option value="fromfile">load from file</option>
	    </param>
	    <when value="fromfile">
		    <param name="bgfile" type="data" format="txt" label="File for background model"/>
	    </when>
    </conditional>
    
      <param name="numseqs" size="10" type="integer" value="20" label="Number of sequences (-numseqs)" help="assume frequencies based on this many sequences; default: 20"/>
    <param name="logodds" label="also output log-odds (PSSM)" help="output the log-odds (PSSM) and frequency (PSPM) motifs; default: PSPM motif only" type="boolean" truevalue="-logodds" falsevalue="" checked="False"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="$motif-meme"/>
  </outputs>
  <help>

**Description**

Convert an IUPAC motif into a MEME version 4 formatted file suitable for use with FIMO and other MEME Suite programs.

See additional information: 

http://meme.sdsc.edu/meme/doc/iupac2meme.html

**IUPAC code**::

    Nucleotide Code:  Base:
    ----------------  -----
    A.................Adenine
    C.................Cytosine
    G.................Guanine
    T (or U)..........Thymine (or Uracil)
    R.................A or G
    Y.................C or T
    S.................G or C
    W.................A or T
    K.................G or T
    M.................A or C
    B.................C or G or T
    D.................A or G or T
    H.................A or C or T
    V.................A or C or G
    N.................any base



  </help>
</tool>