Mercurial > repos > iuc > ebi_search_rest_results
comparison ebi_search_rest_results.xml @ 0:bb7989bd88ba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
author | iuc |
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date | Thu, 01 Dec 2016 15:28:20 -0500 |
parents | |
children | 42d5e40fcd0b |
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1 <tool id="ebi_search_rest_results" name="EBI Search" version="0.1.0"> | |
2 <description>to obtain search results on resources and services hosted at the EBI</description> | |
3 | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 | |
8 <expand macro="requirements" /> | |
9 | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 #set $queries='' | |
12 #set $sep='' | |
13 #for query in $searched_domain.queries: | |
14 #if $sep == '' | |
15 #set $queries = $queries | |
16 #set $sep = str($query.combination_operation) | |
17 #else | |
18 #set $sep = str($query.combination_operation) | |
19 #set $queries += ' %s ' % ($sep) | |
20 #end if | |
21 | |
22 #set $queries += '%s:' % (str($query.query_field)) | |
23 #if str($query.comp_operation.operation) == 'equal' | |
24 #set $queries += '(%s)' % (str($query.comp_operation.query_text)) | |
25 #else if str($query.comp_operation.operation) == 'not' | |
26 #set $queries += '(%s NOT %s)' % (str($query.comp_operation.query_text), str($query.comp_operation.not_query_text)) | |
27 #else if str($query.comp_operation.operation) == 'range' | |
28 #set $queries += '[%s TO %s]' % (str($query.comp_operation.min), str($query.comp_operation.max)) | |
29 #end if | |
30 #end for | |
31 | |
32 python '$__tool_directory__/ebeye_urllib.py' | |
33 getResults | |
34 '$searched_domain.domain' | |
35 '$queries' | |
36 '$searched_domain.fields' | |
37 > '$search_results' | |
38 ]]></command> | |
39 | |
40 <inputs> | |
41 <expand macro="inputs" /> | |
42 </inputs> | |
43 | |
44 <outputs> | |
45 <data name="search_results" format="tabular" label="${tool.name} on ${searched_domain.domain}" /> | |
46 </outputs> | |
47 | |
48 <tests> | |
49 <test> | |
50 <conditional name="searched_domain"> | |
51 <param name="domain" value="metagenomics_runs" /> | |
52 <param name="fields" value="id,experiment_type" /> | |
53 <repeat name="queries"> | |
54 <param name="combination_operation" value="AND" /> | |
55 <param name="query_field" value="biome" /> | |
56 <conditional name="comp_operation"> | |
57 <param name="operation" value="equal" /> | |
58 <param name="query_text" value="gut" /> | |
59 </conditional> | |
60 </repeat> | |
61 </conditional> | |
62 <output name="search_results"> | |
63 <assert_contents> | |
64 <has_line_matching expression="^ERR762518.*" /> | |
65 <has_line_matching expression="^ERR1337677.*" /> | |
66 <has_line_matching expression="^ERR489293.*" /> | |
67 </assert_contents> | |
68 </output> | |
69 </test> | |
70 <test> | |
71 <conditional name="searched_domain"> | |
72 <param name="domain" value="metagenomics_runs" /> | |
73 <param name="fields" value="id,experiment_type" /> | |
74 <repeat name="queries"> | |
75 <param name="combination_operation" value="AND" /> | |
76 <param name="query_field" value="project_name" /> | |
77 <conditional name="comp_operation"> | |
78 <param name="operation" value="not" /> | |
79 <param name="query_text" value="cheese" /> | |
80 <param name="not_query_text" value="microb" /> | |
81 </conditional> | |
82 </repeat> | |
83 </conditional> | |
84 <output name="search_results"> | |
85 <assert_contents> | |
86 <has_line_matching expression="^SRR1205272.*" /> | |
87 <has_line_matching expression="^ERR364233, ERR364234.*" /> | |
88 <has_line_matching expression="^SRR2126380.*" /> | |
89 </assert_contents> | |
90 </output> | |
91 </test> | |
92 <test> | |
93 <conditional name="searched_domain"> | |
94 <param name="domain" value="metagenomics_runs" /> | |
95 <param name="fields" value="id,experiment_type" /> | |
96 <repeat name="queries"> | |
97 <param name="combination_operation" value="AND" /> | |
98 <param name="query_field" value="biome" /> | |
99 <conditional name="comp_operation"> | |
100 <param name="operation" value="equal" /> | |
101 <param name="query_text" value="marine" /> | |
102 </conditional> | |
103 </repeat> | |
104 <repeat name="queries"> | |
105 <param name="combination_operation" value="AND" /> | |
106 <param name="query_field" value="depth" /> | |
107 <conditional name="comp_operation"> | |
108 <param name="operation" value="range" /> | |
109 <param name="min" value="0" /> | |
110 <param name="max" value="200" /> | |
111 </conditional> | |
112 </repeat> | |
113 </conditional> | |
114 <output name="search_results"> | |
115 <assert_contents> | |
116 <has_line_matching expression="^ERR091545,ERR091546,ERR091547,ERR091548.*" /> | |
117 <has_line_matching expression="^ERR771081.*" /> | |
118 <has_line_matching expression="^ERR1278020.*" /> | |
119 </assert_contents> | |
120 </output> | |
121 </test> | |
122 </tests> | |
123 | |
124 <help><![CDATA[ | |
125 **What it does** | |
126 | |
127 The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases. | |
128 | |
129 EBI Search, also named as 'EB-eye', is a scalable search engine that: | |
130 | |
131 - provides text search functionality and uniform access to resources and services hosted at the European Bioinformatics Institute (EMBL-EBI) | |
132 - is based on the consolidated Apache Lucene technology | |
133 - exposes both a Web and RESTful Web Services interfaces | |
134 - provides inter-domain navigation via a network of cross-references | |
135 | |
136 Here, sample clients provided by EBI is used | |
137 ]]></help> | |
138 | |
139 <expand macro="citations" /> | |
140 </tool> |