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1 <tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0">
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2 <description>ClosestToStartSite parses a bed file and generate a report about positions of features A to features B. It can also add the class code of features A.</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">TEiso_Tools</requirement>
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5 </requirements>
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6 <version_command>
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7 ClosestToStartSite.py --version
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8 </version_command>
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9 <command interpreter="python">
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10 #if $ClassCode.get_class_code
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11 ClosestToStartSite_Wrapper.py -i $inputFile -c $cuffcom_tmap -o $outputFile
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12 #else
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13 ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
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14 #end if
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15 </command>
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16 <inputs>
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17 <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
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18 <conditional name="ClassCode">
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19 <param name="get_class_code" type="boolean" label="get information of class code from cuff_in.tmap" truevalue="yes" falsevalue="no" checked="off" />
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20 <when value="no"/>
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21 <when value="yes">
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22 <param name="cuffcom_tmap" type="data" format="tabular" label="indicate cuff_in.tmap" help="default = 1"/>
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23 </when>
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24 </conditional>
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25 </inputs>
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26 <outputs>
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27 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
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28 </outputs>
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29 <help><![CDATA[
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30
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31
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32
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33
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34 **ClosestToStartSite parses a bed file and generate a report about positions of features A (according to its TSS) to features B. It can also add the class code of features A.**
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35
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36 **what it does :**
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37
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38 generate a report about positions of features B to features A (according to its TSS). In input file, there are the information of the two features. ClosestToStartSite reports only the cases that features Bis near to TSS or has overlap with TSS of features A. it can be also run cuffcopare to features A, and add the class code information to output file.
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39
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40
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41 -----
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42
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43 **example :**
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44
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45
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46 Bed input file: ::
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47
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48 2L 239751 240346 CUFF.36.1 CUFF.36 - 2L 239932 241306 RXX + 415 TE_overlap_TSS
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49 2L 113233 113411 CUFF.14.1 CUFF.14 - 2L 113496 113509 RLX - -854 TE_near_TSS
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50
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51
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52 ----
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53
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54 output format: ::
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55
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56
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57 2L 239751 240346 CUFF.36.1 CUFF.36 - 2L 239932 241306 RXX + 415 TE_overlap_TSS
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58 2L 113233 113411 CUFF.14.1 CUFF.14 - 2L 113496 113509 RLX - -854 TE_near_TSS
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59
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60
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61 output format with calss code: ::
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62
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64 2L 239751 240346 CUFF.36.1 CUFF.36 - 2L 239932 241306 RXX + 415 TE_overlap_TSS c gene-id-1
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65 2L 113233 113411 CUFF.14.1 CUFF.14 - 2L 113496 113509 RLX - -854 TE_near_TSS = gene-id-2
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66
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67
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68 ]]>
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69 </help>
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70 </tool>
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