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annotate SMART/galaxy/test/CollapseReads.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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6
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1 <tool id="collapseReads" name="collapseReads">
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2 <description>Merges two reads if they have exactly the same genomic coordinates.</description>
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3 <command interpreter="python">
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4 ../Java/Python/CollapseReads.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 $formatType.FormatInputFileName == 'gff3':
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12 -f gff3
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13 #end if
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14
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15 -$strand
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16 -o $outputFileGff
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17 --galaxy
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18 </command>
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19
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20 <inputs>
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21 <conditional name="formatType">
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22 <param name="FormatInputFileName" type="select" label="Input File Format">
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23 <option value="bed">bed</option>
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24 <option value="gff">gff</option>
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25 <option value="gff2">gff2</option>
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26 <option value="gff3">gff3</option>
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27 </param>
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28 <when value="bed">
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29 <param name="inputFileName" format="bed" type="data" label="Input File"/>
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30 </when>
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31 <when value="gff">
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32 <param name="inputFileName" format="gff" type="data" label="Input File"/>
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33 </when>
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34 <when value="gff2">
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35 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
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36 </when>
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37 <when value="gff3">
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38 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
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39 </when>
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40 </conditional>
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41
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42 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/>
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43 </inputs>
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44
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45 <outputs>
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46 <data name="outputFileGff" format="gff3"/>
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47 </outputs>
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48
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49 </tool>