annotate ebi_search_rest_results.xml @ 3:42d5e40fcd0b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 31d1c92a4c12b6a78693dc5091a08536a075285e
author iuc
date Thu, 09 Feb 2017 12:02:58 -0500
parents bb7989bd88ba
children
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42d5e40fcd0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 31d1c92a4c12b6a78693dc5091a08536a075285e
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1 <tool id="ebi_search_rest_results" name="EBI Search" version="0.1.1">
0
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2 <description>to obtain search results on resources and services hosted at the EBI</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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6 </macros>
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7
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8 <expand macro="requirements" />
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11 #set $queries=''
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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12 #set $sep=''
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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13 #for query in $searched_domain.queries:
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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14 #if $sep == ''
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15 #set $queries = $queries
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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16 #set $sep = str($query.combination_operation)
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17 #else
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18 #set $sep = str($query.combination_operation)
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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19 #set $queries += ' %s ' % ($sep)
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20 #end if
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21
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22 #set $queries += '%s:' % (str($query.query_field))
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23 #if str($query.comp_operation.operation) == 'equal'
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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24 #set $queries += '(%s)' % (str($query.comp_operation.query_text))
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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25 #else if str($query.comp_operation.operation) == 'not'
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26 #set $queries += '(%s NOT %s)' % (str($query.comp_operation.query_text), str($query.comp_operation.not_query_text))
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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27 #else if str($query.comp_operation.operation) == 'range'
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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28 #set $queries += '[%s TO %s]' % (str($query.comp_operation.min), str($query.comp_operation.max))
bb7989bd88ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
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29 #end if
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30 #end for
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31
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32 python '$__tool_directory__/ebeye_urllib.py'
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33 getResults
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34 '$searched_domain.domain'
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35 '$queries'
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36 '$searched_domain.fields'
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37 > '$search_results'
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38 ]]></command>
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39
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40 <inputs>
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41 <expand macro="inputs" />
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42 </inputs>
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43
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44 <outputs>
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45 <data name="search_results" format="tabular" label="${tool.name} on ${searched_domain.domain}" />
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46 </outputs>
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47
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48 <tests>
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49 <test>
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50 <conditional name="searched_domain">
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51 <param name="domain" value="metagenomics_runs" />
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52 <param name="fields" value="id,experiment_type" />
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53 <repeat name="queries">
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54 <param name="combination_operation" value="AND" />
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55 <param name="query_field" value="biome" />
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56 <conditional name="comp_operation">
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57 <param name="operation" value="equal" />
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58 <param name="query_text" value="gut" />
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59 </conditional>
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60 </repeat>
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61 </conditional>
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62 <output name="search_results">
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63 <assert_contents>
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64 <has_line_matching expression="^ERR762518.*" />
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65 <has_line_matching expression="^ERR1337677.*" />
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66 <has_line_matching expression="^ERR489293.*" />
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67 </assert_contents>
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68 </output>
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69 </test>
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70 <test>
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71 <conditional name="searched_domain">
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72 <param name="domain" value="metagenomics_runs" />
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73 <param name="fields" value="id,experiment_type" />
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74 <repeat name="queries">
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75 <param name="combination_operation" value="AND" />
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76 <param name="query_field" value="project_name" />
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77 <conditional name="comp_operation">
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78 <param name="operation" value="not" />
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79 <param name="query_text" value="cheese" />
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80 <param name="not_query_text" value="microb" />
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81 </conditional>
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82 </repeat>
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83 </conditional>
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84 <output name="search_results">
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85 <assert_contents>
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86 <has_line_matching expression="^SRR1205272.*" />
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87 <has_line_matching expression="^ERR364233, ERR364234.*" />
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88 <has_line_matching expression="^SRR2126380.*" />
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89 </assert_contents>
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90 </output>
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91 </test>
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92 <test>
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93 <conditional name="searched_domain">
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94 <param name="domain" value="metagenomics_runs" />
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95 <param name="fields" value="id,experiment_type" />
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96 <repeat name="queries">
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97 <param name="combination_operation" value="AND" />
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98 <param name="query_field" value="biome" />
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99 <conditional name="comp_operation">
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100 <param name="operation" value="equal" />
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101 <param name="query_text" value="marine" />
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102 </conditional>
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103 </repeat>
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104 <repeat name="queries">
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105 <param name="combination_operation" value="AND" />
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106 <param name="query_field" value="depth" />
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107 <conditional name="comp_operation">
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108 <param name="operation" value="range" />
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109 <param name="min" value="0" />
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110 <param name="max" value="200" />
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111 </conditional>
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112 </repeat>
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113 </conditional>
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114 <output name="search_results">
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115 <assert_contents>
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116 <has_line_matching expression="^ERR091545,ERR091546,ERR091547,ERR091548.*" />
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117 <has_line_matching expression="^ERR771081.*" />
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118 <has_line_matching expression="^ERR1278020.*" />
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119 </assert_contents>
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120 </output>
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121 </test>
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122 </tests>
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123
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124 <help><![CDATA[
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125 **What it does**
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126
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127 The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases.
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128
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129 EBI Search, also named as 'EB-eye', is a scalable search engine that:
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130
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131 - provides text search functionality and uniform access to resources and services hosted at the European Bioinformatics Institute (EMBL-EBI)
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132 - is based on the consolidated Apache Lucene technology
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133 - exposes both a Web and RESTful Web Services interfaces
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134 - provides inter-domain navigation via a network of cross-references
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135
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136 Here, sample clients provided by EBI is used
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137 ]]></help>
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138
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139 <expand macro="citations" />
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140 </tool>