annotate enasearch_search_data.xml @ 2:63b13eb2cb8a draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit a0adc28145cce02ecaed3a90156ed54c4385d1a0"

<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">
                <assert_contents>
                    <has_text text=">ENA|" />
                    <has_text text="MUTATIONS ASSOCIATED WITH RESISTANCE TO INHIBITORS OF BRUTON" />
                </assert_contents>
            </output>
        </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">
                <assert_contents>
                    <has_text text="entry accession=&quot;AAA02481&quot;" />
                    <has_text text="entry accession=&quot;AAA02488&quot;" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool retrieve ENA taxon data
    ]]></help>
    <expand macro="citations"/>
</tool>