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annotate macros.xml @ 83:0bc486356e2a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
author yating-l
date Mon, 30 Oct 2017 12:01:23 -0400
parents 2440ce10848b
children cb62314a6297
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1 <macros>
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2 <xml name="verify_hub_structure" token_genome="Dbia3" token_test="common">
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3 <!--genomes.txt -->
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4 <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" />
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5
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6 <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/>
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7 <!-- hub.txt -->
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8 <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2">
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9 <assert_contents>
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10 <has_text text="email"/>
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11 </assert_contents>
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12 </extra_files>
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13 <!-- 2bit file -->
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14 <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" />
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15 <!-- groups.txt -->
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16 <extra_files type="file" name="myHub/@GENOME@/groups.txt" value="@TEST@/myHub/@GENOME@/groups.txt" />
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17 <!-- description.html -->
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18 <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/>
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19 <!-- trackDb.txt -->
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20 <extra_files type="file" name="myHub/@GENOME@/trackDb.txt">
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21 <assert_contents>
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22 <has_text text="track"/>
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23 <has_text text="longLabel"/>
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24 <has_text text="shortLabel"/>
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25 <has_text text="bigDataUrl"/>
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26 <has_text text="type"/>
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27 <has_text text="visibility"/>
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28 <has_text text="thickDrawItem"/>
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29 <has_text text="priority"/>
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30 <has_text text="color"/>
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31 <has_text text="group"/>
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32 </assert_contents>
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33 </extra_files>
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34 </xml>
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35
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36 <xml name="verify_hub_structure_no_track" token_genome="Dbia3" token_test="common">
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37 <!--genomes.txt -->
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38 <extra_files type="file" name="myHub/genomes.txt" value="@TEST@/myHub/genomes.txt" />
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39
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40 <extra_files type="file" name="myHub/@GENOME@.html" value="@TEST@/myHub/@GENOME@.html"/>
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41 <!-- hub.txt -->
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42 <extra_files type="file" name="myHub/hub.txt" value="@TEST@/myHub/hub.txt" lines_diff="2">
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43 <assert_contents>
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44 <has_text text="email"/>
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45 </assert_contents>
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46 </extra_files>
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47 <!-- 2bit file -->
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48 <extra_files type="file" name="myHub/@GENOME@/@GENOME@.2bit" value="common/@GENOME@.2bit" />
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49 <!-- description.html -->
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50 <extra_files type="file" name="myHub/@GENOME@/description.html" value="@TEST@/myHub/@GENOME@/description.html"/>
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51 </xml>
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52
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53 <xml name="add_trix_file">
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54 <conditional name="add_trix_index">
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55 <param name="add_trix_index_selector" type="select" label="Add Trix index that allow for fast look-up of free text associated with a list of identifiers." help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html">
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56 <option value="no" selected="true">No</option>
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57 <option value="yes">Yes</option>
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58 </param>
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59
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60 <when value="yes">
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61 <param
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62 name="trix_index"
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63 format="txt"
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64 type="data_collection"
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65 collection_type="list"
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66 label="Specify Trix index"
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67 help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator"
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68 />
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69 <yield />
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70 </when>
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71 <when value="no">
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72 </when>
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73 </conditional>
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74 </xml>
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75
66
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76 </macros>