Mercurial > repos > devteam > ucsc_custom_track

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
author devteam
date Mon, 28 Feb 2022 20:05:39 +0000
parents 2e057d4433b2
children
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rev   line source
2
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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1 <tool id="build_ucsc_custom_track_1" name="Build custom track" version="1.0.1" profile="21.01">
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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2 <description>for UCSC genome browser</description>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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3 <requirements>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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4 <requirement type="package" version="3.10">python</requirement>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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5 </requirements>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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6 <code file="build_ucsc_custom_track_code.py" />
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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7 <command detect_errors="exit_code"><![CDATA[
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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8 python '$__tool_directory__/build_ucsc_custom_track.py'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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9 '$out_file1'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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10 #for $t in $tracks
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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11 '${t.input.file_name}'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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12 '${t.input.ext}'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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13 #if $t.input.ext == "interval"
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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14 '${t.input.metadata.chromCol},${t.input.metadata.startCol},${t.input.metadata.endCol},${t.input.metadata.strandCol}'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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15 #else
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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16 "NA"
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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17 #end if
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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18 '${t.name}'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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19 '${t.description}'
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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20 "${t.color}"
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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21 ${t.visibility}
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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22 #end for
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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23 ]]></command>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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24 <inputs>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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25 <repeat name="tracks" title="Track">
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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26 <param name="input" type="data" format="interval,wig" label="Dataset"/>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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27 <param name="name" type="text" value="User Track">
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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28 <validator type="length" max="15"/>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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29 </param>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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30 <param name="description" type="text" value="User Supplied Track (from Galaxy)">
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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31 <validator type="length" max="60"/>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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32 </param>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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33 <param name="color" type="select" label="Color">
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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34 <option selected="yes" value="0-0-0">Black</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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35 <option value="255-0-0">Red</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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36 <option value="0-255-0">Green</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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37 <option value="0-0-255">Blue</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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38 <option value="255-0-255">Magenta</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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39 <option value="0-255-255">Cyan</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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40 <option value="255-215-0">Gold</option>
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41 <option value="160-32-240">Purple</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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42 <option value="255-140-0">Orange</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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43 <option value="255-20-147">Pink</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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44 <option value="92-51-23">Dark Chocolate</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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45 <option value="85-107-47">Olive green</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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46 </param>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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47 <param name="visibility" type="select" label="Visibility">
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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48 <option selected="yes" value="1">Dense</option>
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49 <option value="2">Full</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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50 <option value="3">Pack</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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51 <option value="4">Squish</option>
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52 <option value="0">Hide</option>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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53 </param>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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54 </repeat>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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55 </inputs>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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56 <outputs>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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57 <data name="out_file1" format="customtrack" />
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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58 </outputs>
0
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59 <tests>
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60 <!--TODO: add a 2nd test here that includes 2 tracks -->
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61 <test>
2
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62 <param name="input" value="customTrack1.bed" />
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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63 <param name="name" value="User Track" />
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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64 <param name="description" value="User Supplied Track (from Galaxy)" />
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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65 <param name="color" value="0-0-0" />
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66 <param name="visibility" value="1" />
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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67 <output name="out_file1" file="build_ucsc_custom_track_out1.customtrack" />
0
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68 </test>
2
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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69 </tests>
f1fd9e6e026e "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
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70 <help><![CDATA[
0
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71 .. class:: infomark
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72
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73 This tool allows you to build custom tracks using datasets in your history for the UCSC genome browser. You can view these custom tracks on the UCSC genome browser by clicking on **display at UCSC main/test** link in the history panel of the output dataset.
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74
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75 -----
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76
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77 .. class:: warningmark
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78
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79 Please note that this tool requires **all input datasets(tracks) to have the same genome build**. The tool throws an error when this requirement is not met. You may then have to choose a valid dataset or remove invalid tracks.
2
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80 ]]></help>
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81 </tool>