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1 <tool id="fimo" name="motif search">
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2 <description>using FIMO</description>
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3 <command> fimo
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4 #if $background_select.bg_select == "fromfile":
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5 -bgfile $bgfile
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6 #end if
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7
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8 $norc --output-pthresh $pth --verbosity 1 $motif $database
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9 && mv fimo_out/fimo.html ${html_outfile}
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10
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11 && mv fimo_out/fimo.txt ${txt_outfile}
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12
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13 && rm -rf fimo_out
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14
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15 </command>
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16 <inputs>
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17 <conditional name="motif_selection">
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18 <param name="motif_sel" type="select" label="Motif Source">
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19 <option value="user" selected="true">Use motif file in Your History</option>
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20 <option value="known" >Known motif</option>
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21 </param>
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22 ##<when value="known">
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23 ## <param name="motif" type="select" label="Select motif">
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24 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite" selected="true">mouse 5 primer splice site</option>
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25 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/5primerSpliceSite">mouse 3 primer splice site</option>
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26 ## <option value="/Users/xuebing/galaxy-dist/tool-data/motif-database/TATA-Box.meme">TATA box</option>
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27 ## </param>
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28 ##</when>
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29 <when value="user">
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30 <param name="motif" type="data" format="txt" label="Motif file" help="created using the tool create-motif-file, or import from Shared Data"/>
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31 </when>
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32 </conditional>
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33
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34 <param name="database" type="data" format="fasta" label="Sequence file (FASTA)"/>
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35
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36 <conditional name="background_select">
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37 <param name="bg_select" type="select" label="Background model" >
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38 <option value="uniform" selected="true">uniform</option>
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39 <option value="fromfile">load from file</option>
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40 </param>
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41 <when value="fromfile">
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42 <param name="bgfile" type="data" format="txt" label="File for background model"/>
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43 </when>
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44 </conditional>
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45
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46 <param name="pth" size="10" type="float" value="0.01" label="p-value threshold"/>
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47 <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"/>
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
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51 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (txt)"/>
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52 </outputs>
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53 <help>
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54
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55 **What it does**
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56
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57 This tool uses FIMO to find matches of a motif in a fasta file. See more details:
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58
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59 http://meme.sdsc.edu/meme/fimo-intro.html
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60
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61
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62 </help>
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63 </tool>
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