| Previous changeset 1:cdcb0ce84a1b (2012-03-09) Next changeset 3:33c067c3ae34 (2012-03-09) |
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added:
fimo2.xml |
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| diff -r cdcb0ce84a1b -r c2a356708570 fimo2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fimo2.xml Fri Mar 09 19:45:42 2012 -0500 |
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| @@ -0,0 +1,47 @@ +<tool id="fimo" name="motif search"> + <description>using FIMO</description> + <command> fimo + #if $background_select.bg_select == "fromfile": + -bgfile $bgfile + #end if + + $norc --max-stored-scores 5000000 --output-pthresh $pth --verbosity 1 $motif $database + && mv fimo_out/fimo.html ${html_outfile} + + && mv fimo_out/fimo.txt ${txt_outfile} + + && rm -rf fimo_out + + </command> + <inputs> + + <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/> + <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/> + + <conditional name="background_select"> + <param name="bg_select" type="select" label="Background model" > + <option value="uniform" selected="true">uniform</option> + <option value="fromfile">load from file</option> + </param> + <when value="fromfile"> + <param name="bgfile" type="data" format="txt" label="File for background model"/> + </when> + </conditional> + + <param name="pth" size="10" type="float" value="0.0001" label="p-value threshold"/> + <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/> + </inputs> + <outputs> + <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/> + <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/> + </outputs> + <help> + +**What it does** + +This tool uses FIMO to find matches of a motif in a fasta file. See more details: + +http://meme.sdsc.edu/meme/fimo-intro.html + + </help> +</tool> |