diff enasearch_search_data.xml @ 0:fc42e7901a23 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/enasearch_search_data.xml	Tue Aug 29 04:13:28 2017 -0400
@@ -0,0 +1,143 @@
+<tool id="enasearch_search_data" name="Search ENA data" version="@WRAPPER_VERSION@.0">
+    <description>given a query</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>search_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="aggressive"><![CDATA[
+enasearch
+    search_data
+    $query_type.free_text_search
+    #if $query_type.free_text_search == '--free_text_search'
+        --query '$query_type.query'
+        --result '$query_type.res.result'
+        @SEARCH_DATA_DISPLAY@
+    #else
+        --result '$query_type.res.result'
+        #set $queries=''
+        #set $sep=''
+        #for $i, $s in enumerate( $query_type.res.queries )
+            #if $sep == ''
+                #set $sep = str($s.combination_operation)
+            #else
+                #set $sep = str($s.combination_operation)
+                #set $queries += ' %s ' % ($sep)
+            #end if
+            #if $s.filter_field.field != 'location'
+                #set $queries += '%s' % (str($s.filter_field.field))
+                #if str($s.filter_field.operation) == "equal"
+                    #set $queries += '='
+                #elif str($s.filter_field.operation) == "different"
+                    #set $queries += '!='
+                #elif str($s.filter_field.operation) == "lower"
+                    #set $queries += '<'
+                #elif str($s.filter_field.operation) == "equal or lower"
+                    #set $queries += '<='
+                #elif str($s.filter_field.operation) == "higher"
+                    #set $queries += '>'
+                #elif str($s.filter_field.operation) == "equal or higher"
+                    #set $queries += '>='
+                #end if
+                #set $queries += '"%s"' % (str($s.filter_field.value))
+            #else
+                #set $queries += '%s(%s)' % (str($s.filter_field.operation),str($s.filter_field.values))
+            #end if
+        #end for
+        --query '$queries'
+        @SEARCH_DATA_DISPLAY@
+    #end if
+    --file '$output'
+    --download 'txt'
+    ]]></command>
+    <inputs>
+        <conditional name="query_type">
+            <param argument="--free_text_search" type="select" label="Use free text search?" help="If not, the ENA data warehouse is used">
+                <option value="--free_text_search">Yes</option>
+                <option value="">False</option>
+            </param>
+            <when value="--free_text_search">
+                <param argument="--query" type="text" label="Query"/>
+                <expand macro="free_text_search"/>
+            </when>
+            <when value="">
+                <expand macro="conditional_text_search"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name}">
+            <change_format>
+                <when input="query_type.res.display_opt.display" value="fasta" format="fasta" />
+                <when input="query_type.res.display_opt.display" value="fastq" format="fastq" />
+                <when input="query_type.res.display_opt.display" value="html" format="html" />
+                <when input="query_type.res.display_opt.display" value="text" format="text" />
+                <when input="query_type.res.display_opt.display" value="xml" format="xml" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="query_type">
+                <param name="free_text_search" value="--free_text_search"/>
+                <param name="query" value="kinase+homo+sapiens"/>
+                <conditional name="res">
+                    <param name="result" value="sequence_update"/>
+                    <conditional name="display_opt">
+                        <param name="display" value="fasta"/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="output" ftype="fasta" md5="d02da99308bbf1e432fc5614c1982994"/>
+        </test>
+        <test>
+            <conditional name="query_type">
+                <param name="free_text_search" value="--free_text_search"/>
+                <param name="query" value="kinase+homo+sapiens"/>
+                <conditional name="res">
+                    <param name="result" value="wgs_set"/>
+                    <conditional name="display_opt">
+                        <param name="display" value="report"/>
+                        <param name="fields" value="accession,environmental_sample"/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="output" ftype="tabular" md5="c1f91a8276f59c90ec53025e1a3d31d5"/>
+        </test>
+        <test>
+            <conditional name="query_type">
+                <param name="free_text_search" value=""/>
+                <conditional name="res">
+                    <param name="result" value="coding_release"/>
+                    <repeat name="queries">
+                        <param name="combination_operation" value="AND"/>
+                        <conditional name="filter_field">
+                            <param name="field" value="dataclass"/>
+                            <param name="operation" value="equal"/>
+                            <param name="value" value="STD"/>
+                        </conditional>
+                    </repeat>
+                    <repeat name="queries">
+                        <param name="combination_operation" value="AND"/>
+                        <conditional name="filter_field">
+                            <param name="field" value="tissue_lib"/>
+                            <param name="operation" value="equal"/>
+                            <param name="value" value="lambda gt11"/>
+                        </conditional>
+                    </repeat>
+                    <conditional name="display_opt">
+                        <param name="display" value="xml"/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="output" ftype="xml" md5="0ed405b4db2bcaf9c1540307fe15e9bb"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool retrieve ENA taxon data
+    ]]></help>
+    <expand macro="citations"/>
+</tool>