Mercurial > repos > yating-l > hubarchivecreatortest

annotate macros.xml @ 1:85195e0d4b71 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
author yating-l
date Fri, 29 Sep 2017 13:32:23 -0400
parents
children 7486909dfc22
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
85195e0d4b71 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
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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 files that maps free text to a set of indices" >
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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_id"
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63 value="name"
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64 type="text"
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65 size="30"
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66 label="Specify Trix identifier"
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67 help="More about Trix index: https://genome.ucsc.edu/goldenpath/help/trix.html"
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68 />
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69 <conditional name="index_files">
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70 <param name="index_files_type" type="select" label="Single files or an index collection" help="Select between provide individual trix files (ix and ixx) or an trix index collection">
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71 <option value="collection">Index collection</option>
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72 <option value="single">Single files</option>
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73 </param>
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74 <when value="collection">
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75 <param
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76 name="index_collection"
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77 format="txt"
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78 type="data_collection"
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79 collection_type="list"
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80 label="Select dataset collection"
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81 help="Specify dataset collection containing ix and ixx files"
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82 />
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83 </when>
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84 <when value="single">
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85 <param
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86 format="txt"
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87 name="index_ix"
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88 type="data"
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89 label="Trix index file (ix)"
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90 />
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91 <param
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92 format="txt"
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93 name="index_ixx"
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94 type="data"
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95 label="Trix index file (ixx)"
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96 />
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97 </when>
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98 </conditional>
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99 </when>
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100 <when value="no">
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101 </when>
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102 </conditional>
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103 </xml>
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104
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105 </macros>