Mercurial > repos > iuc > ebi_search_rest_results
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebi_search_rest_results.xml Thu Dec 01 15:28:20 2016 -0500 @@ -0,0 +1,140 @@ +<tool id="ebi_search_rest_results" name="EBI Search" version="0.1.0"> + <description>to obtain search results on resources and services hosted at the EBI</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + + <command detect_errors="exit_code"><![CDATA[ + #set $queries='' + #set $sep='' + #for query in $searched_domain.queries: + #if $sep == '' + #set $queries = $queries + #set $sep = str($query.combination_operation) + #else + #set $sep = str($query.combination_operation) + #set $queries += ' %s ' % ($sep) + #end if + + #set $queries += '%s:' % (str($query.query_field)) + #if str($query.comp_operation.operation) == 'equal' + #set $queries += '(%s)' % (str($query.comp_operation.query_text)) + #else if str($query.comp_operation.operation) == 'not' + #set $queries += '(%s NOT %s)' % (str($query.comp_operation.query_text), str($query.comp_operation.not_query_text)) + #else if str($query.comp_operation.operation) == 'range' + #set $queries += '[%s TO %s]' % (str($query.comp_operation.min), str($query.comp_operation.max)) + #end if + #end for + + python '$__tool_directory__/ebeye_urllib.py' + getResults + '$searched_domain.domain' + '$queries' + '$searched_domain.fields' + > '$search_results' + ]]></command> + + <inputs> + <expand macro="inputs" /> + </inputs> + + <outputs> + <data name="search_results" format="tabular" label="${tool.name} on ${searched_domain.domain}" /> + </outputs> + + <tests> + <test> + <conditional name="searched_domain"> + <param name="domain" value="metagenomics_runs" /> + <param name="fields" value="id,experiment_type" /> + <repeat name="queries"> + <param name="combination_operation" value="AND" /> + <param name="query_field" value="biome" /> + <conditional name="comp_operation"> + <param name="operation" value="equal" /> + <param name="query_text" value="gut" /> + </conditional> + </repeat> + </conditional> + <output name="search_results"> + <assert_contents> + <has_line_matching expression="^ERR762518.*" /> + <has_line_matching expression="^ERR1337677.*" /> + <has_line_matching expression="^ERR489293.*" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="searched_domain"> + <param name="domain" value="metagenomics_runs" /> + <param name="fields" value="id,experiment_type" /> + <repeat name="queries"> + <param name="combination_operation" value="AND" /> + <param name="query_field" value="project_name" /> + <conditional name="comp_operation"> + <param name="operation" value="not" /> + <param name="query_text" value="cheese" /> + <param name="not_query_text" value="microb" /> + </conditional> + </repeat> + </conditional> + <output name="search_results"> + <assert_contents> + <has_line_matching expression="^SRR1205272.*" /> + <has_line_matching expression="^ERR364233, ERR364234.*" /> + <has_line_matching expression="^SRR2126380.*" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="searched_domain"> + <param name="domain" value="metagenomics_runs" /> + <param name="fields" value="id,experiment_type" /> + <repeat name="queries"> + <param name="combination_operation" value="AND" /> + <param name="query_field" value="biome" /> + <conditional name="comp_operation"> + <param name="operation" value="equal" /> + <param name="query_text" value="marine" /> + </conditional> + </repeat> + <repeat name="queries"> + <param name="combination_operation" value="AND" /> + <param name="query_field" value="depth" /> + <conditional name="comp_operation"> + <param name="operation" value="range" /> + <param name="min" value="0" /> + <param name="max" value="200" /> + </conditional> + </repeat> + </conditional> + <output name="search_results"> + <assert_contents> + <has_line_matching expression="^ERR091545,ERR091546,ERR091547,ERR091548.*" /> + <has_line_matching expression="^ERR771081.*" /> + <has_line_matching expression="^ERR1278020.*" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases. + +EBI Search, also named as 'EB-eye', is a scalable search engine that: + +- provides text search functionality and uniform access to resources and services hosted at the European Bioinformatics Institute (EMBL-EBI) +- is based on the consolidated Apache Lucene technology +- exposes both a Web and RESTful Web Services interfaces +- provides inter-domain navigation via a network of cross-references + +Here, sample clients provided by EBI is used + ]]></help> + + <expand macro="citations" /> +</tool>