annotate einfo.xml @ 2:df0df73c8bda draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b

<tool id="ncbi_entrez_direct_einfo" name="NCBI EInfo" version="@TOOL_VERSION@">
    <description>fetch NCBI database metadata</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>einfo -version</version_command>
    <command detect_errors="exit_code"><![CDATA[
      @ECONTACT@
      einfo
      #if str( $db.target ) == "dbs":
          -dbs
      #else:
          -db "${db.db}"
      #end if
      > '${output_xml}'
      ]]>  
</command>
    <inputs>
        <conditional name="db">
            <param name="target" type="select" label="List DBs or Info on a DB">
                <option value="db" selected="True">DB info</option>
                <option value="dbs">List of DBs</option>
            </param>
            <when value="dbs"/>
            <when value="db">
                <param argument="-db" type="select" label="Choose your DB">
                    <option value="annotinfo">annotinfo</option>
                    <option value="assembly">assembly</option>
                    <option value="bioproject">bioproject</option>
                    <option value="biosample">biosample</option>
                    <option value="biosystems">biosystems</option>
                    <option value="blastdbinfo">blastdbinfo</option>
                    <option value="books">books</option>
                    <option value="cdd">cdd</option>
                    <option value="clinvar">clinvar</option>
                    <option value="clone">clone</option>
                    <option value="dbvar">dbvar</option>
                    <option value="gap">gap</option>
                    <option value="gapplus">gapplus</option>
                    <option value="gds">gds</option>
                    <option value="gencoll">gencoll</option>
                    <option value="gene">gene</option>
                    <option value="genome">genome</option>
                    <option value="geoprofiles">geoprofiles</option>
                    <option value="grasp">grasp</option>
                    <option value="gtr">gtr</option>
                    <option value="homologene">homologene</option>
                    <option value="medgen">medgen</option>
                    <option value="mesh">mesh</option>
                    <option value="ncbisearch">ncbisearch</option>
                    <option value="nlmcatalog">nlmcatalog</option>
                    <option value="nuccore">nuccore</option>
                    <option value="nucest">nucest</option>
                    <option value="nucgss">nucgss</option>
                    <option value="nucleotide">nucleotide</option>
                    <option value="omim">omim</option>
                    <option value="orgtrack">orgtrack</option>
                    <option value="pcassay">pcassay</option>
                    <option value="pccompound">pccompound</option>
                    <option value="pcsubstance">pcsubstance</option>
                    <option value="pmc">pmc</option>
                    <option value="popset">popset</option>
                    <option value="probe">probe</option>
                    <option value="protein">protein</option>
                    <option value="proteinclusters">proteinclusters</option>
                    <option value="pubmed">pubmed</option>
                    <option value="pubmedhealth">pubmedhealth</option>
                    <option value="seqannot">seqannot</option>
                    <option value="snp">snp</option>
                    <option value="sra">sra</option>
                    <option value="structure">structure</option>
                    <option value="taxonomy">taxonomy</option>
                    <option value="unigene">unigene</option>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="xml" name="output_xml"/>
    </outputs>
    <tests>
        <test>
            <param name="db|target" value="db"/>
            <param name="db|db" value="sra"/>
            <output name="output_xml">
                <assert_contents>
                    <has_text_matching expression="SRA"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
NCBI Entrez EInfo
=================

Provides the number of records indexed in each field of a given database, the
date of the last update of the database, and the available links from the
database to other Entrez databases.

@DISCLAIMER@
      ]]></help>
    <expand macro="citations"/>
</tool>