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annotate flanking_features.xml @ 2:a09d13b108fd draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:16 -0400
parents 90100b587723
children
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1 <tool id="flanking_features_1" name="Fetch closest non-overlapping feature" version="4.0.1">
2
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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2 <description>for every interval</description>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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3 <macros>
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4 <import>macros.xml</import>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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5 </macros>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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6 <expand macro="requirements" />
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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7 <command><![CDATA[
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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8 python '$__tool_directory__/flanking_features.py'
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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9 '$input1'
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 '$input2'
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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11 '$out_file1'
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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12 $direction
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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13
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 #if $input1.is_of_type('gff')
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 -1 1,4,5,7 --gff1
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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16 #else:
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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17 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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18 #end if
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19
2
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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20 #if $input2.is_of_type('gff')
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 -2 1,4,5,7 --gff2
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 #else:
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 #end if
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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25 ]]></command>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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26 <inputs>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 <param name="input1" type="data" format="interval,gff" label="For every interval in"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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28 <param name="input2" type="data" format="interval,gff" label="Fetch closest feature(s) from"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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29 <param name="direction" type="select" label="Located">
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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30 <option value="Either">Either Upstream or Downstream</option>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 <option value="Both">Both Upstream and Downstream</option>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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32 <option value="Upstream">Upstream</option>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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33 <option value="Downstream">Downstream</option>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 </param>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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35 </inputs>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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36 <outputs>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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37 <data name="out_file1" format_source="input1" metadata_source="input1"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 </outputs>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 <tests>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 <test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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41 <param name="input1" value="4_windows.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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42 <param name="input2" value="4_windows_2.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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43 <param name="direction" value="Either"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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44 <output name="out_file1" file="closest_features_either.interval"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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45 </test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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46 <test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 <param name="input1" value="4_windows.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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48 <param name="input2" value="4_windows_2.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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49 <param name="direction" value="Both"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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50 <output name="out_file1" file="closest_features.interval"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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51 </test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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52 <test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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53 <param name="input1" value="4_windows.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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54 <param name="input2" value="4_windows_2.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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55 <param name="direction" value="Upstream"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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56 <output name="out_file1" file="closest_features_up.interval"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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57 </test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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58 <test>
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59 <param name="input1" value="4_windows.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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60 <param name="input2" value="4_windows_2.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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61 <param name="direction" value="Downstream"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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62 <output name="out_file1" file="closest_features_down.interval"/>
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63 </test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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64 <test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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65 <param name="input1" value="4_windows.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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66 <param name="input2" value="4_windows_3.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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67 <param name="direction" value="Both"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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68 <output name="out_file1" file="closest_features_both.interval"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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69 </test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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70 <!-- Tests for GFF functionality. -->
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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71 <test>
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72 <param name="input1" value="4_windows.bed"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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73 <param name="input2" value="4_windows_2.gff" ftype="gff" />
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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74 <param name="direction" value="Either"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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75 <output name="out_file1" file="closest_features_both.gff"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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76 </test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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77 <test>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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78 <param name="input1" value="4_windows.gff" ftype="gff" />
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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79 <param name="input2" value="4_windows_2.gff" ftype="gff" />
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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80 <param name="direction" value="Either"/>
a09d13b108fd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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81 <output name="out_file1" file="closest_features_both2.gff"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
0
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85 .. class:: infomark
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86
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87 **What it does**
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88
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89 For every interval in the **interval** dataset, this tool fetches the **closest non-overlapping** upstream and / or downstream features from the **features** dataset.
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90
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91 -----
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92
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93 .. class:: warningmark
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94
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95 **Note:**
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96
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97 Every line should contain at least 3 columns: chromosome number, start and stop coordinates. If any of these columns is missing or if start and stop coordinates are not numerical, the lines will be treated as invalid and skipped. The number of skipped lines is documented in the resulting history item as a "data issue".
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98
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99 If the strand column is missing from your input interval dataset, the intervals will be considered to be on positive strand. You can add a strand column to your input dataset by using the *Text Manipulation->Add column* tool.
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100
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101 For GFF files, features are added as a GTF-style attribute at the end of the line.
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102
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103 -----
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104
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105 **Example**
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106
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107 If the **intervals** are::
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108
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109 chr1 10 100 Query1.1
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110 chr1 500 1000 Query1.2
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111 chr1 1100 1250 Query1.3
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112
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113 and the **features** are::
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114
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115 chr1 120 180 Query2.1
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116 chr1 140 200 Query2.2
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117 chr1 580 1050 Query2.3
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118 chr1 2000 2204 Query2.4
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119 chr1 2500 3000 Query2.5
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120
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121 Running this tool for **Both Upstream and Downstream** will return::
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122
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123 chr1 10 100 Query1.1 chr1 120 180 Query2.1
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124 chr1 500 1000 Query1.2 chr1 140 200 Query2.2
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125 chr1 500 1000 Query1.2 chr1 2000 2204 Query2.4
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126 chr1 1100 1250 Query1.3 chr1 580 1050 Query2.3
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127 chr1 1100 1250 Query1.3 chr1 2000 2204 Query2.4
2
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128 ]]></help>
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129 </tool>