Mercurial > repos > xuebing > iupac_to_meme
changeset 0:55fee32727a9 default tip
Uploaded
| author | xuebing |
|---|---|
| date | Sat, 31 Mar 2012 21:41:37 -0400 |
| parents | |
| children | |
| files | iupac_to_meme.xml |
| diffstat | 1 files changed, 59 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iupac_to_meme.xml Sat Mar 31 21:41:37 2012 -0400 @@ -0,0 +1,59 @@ +<tool id="iupac_to_meme" name="create_MEME_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>