Mercurial > repos > xuebing > sharplabtool
comparison mytools/fimo2.xml @ 7:f0dc65e7f6c0
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:59:07 -0500 |
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| 6:094f377db4e5 | 7:f0dc65e7f6c0 |
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| 1 <tool id="fimo" name="motif search"> | |
| 2 <description>using FIMO</description> | |
| 3 <command> fimo | |
| 4 #if $background_select.bg_select == "fromfile": | |
| 5 -bgfile $bgfile | |
| 6 #end if | |
| 7 | |
| 8 $norc --max-stored-scores 5000000 --output-pthresh $pth --verbosity 1 $motif $database | |
| 9 && mv fimo_out/fimo.html ${html_outfile} | |
| 10 | |
| 11 && mv fimo_out/fimo.txt ${txt_outfile} | |
| 12 | |
| 13 && rm -rf fimo_out | |
| 14 | |
| 15 </command> | |
| 16 <inputs> | |
| 17 | |
| 18 <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/> | |
| 19 <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/> | |
| 20 | |
| 21 <conditional name="background_select"> | |
| 22 <param name="bg_select" type="select" label="Background model" > | |
| 23 <option value="uniform" selected="true">uniform</option> | |
| 24 <option value="fromfile">load from file</option> | |
| 25 </param> | |
| 26 <when value="fromfile"> | |
| 27 <param name="bgfile" type="data" format="txt" label="File for background model"/> | |
| 28 </when> | |
| 29 </conditional> | |
| 30 | |
| 31 <param name="pth" size="10" type="float" value="0.0001" label="p-value threshold"/> | |
| 32 <param name="norc" label="Do not score the reverse complement DNA strand. Both strands are scored by default" type="boolean" truevalue="-norc" falsevalue="" checked="False"/> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/> | |
| 36 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/> | |
| 37 </outputs> | |
| 38 <help> | |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 This tool uses FIMO to find matches of a motif in a fasta file. See more details: | |
| 43 | |
| 44 http://meme.sdsc.edu/meme/fimo-intro.html | |
| 45 | |
| 46 </help> | |
| 47 </tool> |