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annotate SMART/galaxy/plotGenomeCoverage.xml @ 13:03045debed6e

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author m-zytnicki
date Wed, 17 Apr 2013 10:39:35 -0400
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1 <tool id="plotGenomeCoverage" name="plot genome coverage">
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2 <description>Get the coverage of a genome. </description>
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3 <command interpreter="python"> ../Java/Python/plotGenomeCoverage.py -i $formatType.inputFileName
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4 #if $formatType.FormatInputFileName == 'bed':
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5 -f bed
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6 #elif $formatType.FormatInputFileName == 'gff':
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7 -f gff
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8 #elif $formatType.FormatInputFileName == 'gff2':
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9 -f gff2
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10 #elif $formatType.FormatInputFileName == 'gff3':
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11 -f gff3
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12 #elif $formatType.FormatInputFileName == 'sam':
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13 -f sam
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14 #elif $formatType.FormatInputFileName == 'gtf':
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15 -f gtf
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16 #end if
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17
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18 -r $reference
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19 -o $outputFile
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20 </command>
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21
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22
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23 <inputs>
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24 <conditional name="formatType">
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25 <param name="FormatInputFileName" type="select" label="Input File Format">
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26 <option value="bed">bed</option>
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27 <option value="gff">gff</option>
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28 <option value="gff2">gff2</option>
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29 <option value="gff3">gff3</option>
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30 <option value="sam">sam</option>
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31 <option value="gtf">gtf</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 <when value="sam">
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46 <param name="inputFileName" format="sam" type="data" label="Input File"/>
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47 </when>
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48 <when value="gtf">
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49 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
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50 </when>
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51 </conditional>
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52
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53 <param name="reference" type="data" label="reference Fasta File" format="fasta"/>
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54 </inputs>
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55
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56 <outputs>
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57 <data format="png" name="outputFile" label="[plotGenomeCoverage] Output File"/>
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58 </outputs>
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59
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60 <help>
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61 </help>
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62 </tool>