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

--- /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>