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annotate SMART/galaxy/getWigProfile.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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1 <tool id="getWigProfile" name="get wig profile">
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2 <description>Compute the average profile of some genomic coordinates using WIG files (thus covering a large proportion of the genome).</description>
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3 <command interpreter="python">
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4 ../Java/Python/getWigProfile.py -i $formatType.inputFileName
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5 #if $formatType.FormatInputFileName == 'bed':
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6 -f bed
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7 #elif $formatType.FormatInputFileName == 'gff':
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8 -f gff
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9 #elif $formatType.FormatInputFileName == 'gff2':
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10 -f gff2
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11 #elif $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #end if
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14 -w $inputWigFile
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15 -p $nbPoints
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16 -d $distance
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17 $strands
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18 -o $outputFilePNG
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19 #if $optionSMO.SMO == 'Yes':
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20 -m $optionSMO.smoothen
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21 #end if
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22
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23 </command>
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24
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25 <inputs>
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26 <conditional name="formatType">
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27 <param name="FormatInputFileName" type="select" label="Input File Format">
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28 <option value="bed">bed</option>
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29 <option value="gff">gff</option>
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30 <option value="gff2">gff2</option>
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31 <option value="gff3">gff3</option>
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32 </param>
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33 <when value="bed">
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34 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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35 </when>
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36 <when value="gff">
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37 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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38 </when>
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39 <when value="gff2">
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40 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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41 </when>
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42 <when value="gff3">
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43 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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44 </when>
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45 </conditional>
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46
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47 <param name="inputWigFile" type="data" label="Input Wig File" format="wig"/>
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48 <param name="nbPoints" type="integer" value="1000" label="number of points on the x-axis"/>
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49 <param name="distance" type="integer" value="0" label="distance around genomic coordinates"/>
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50 <param name="strands" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately"/>
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51
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52 <conditional name="optionSMO">
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53 <param name="SMO" type="select" label="smoothen the curve">
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54 <option value="Yes">Yes</option>
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55 <option value="No" selected="true">No</option>
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56 </param>
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57 <when value="Yes">
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58 <param name="smoothen" type="integer" value="0"/>
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59 </when>
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60 <when value="No">
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61 </when>
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62 </conditional>
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64 </inputs>
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65
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66 <outputs>
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67 <data name="outputFilePNG" format="png" label="[getWigProfile]out file"/>
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68 </outputs>
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70 </tool>