annotate einfo.xml @ 9:6a0463d18db2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0

<tool id="ncbi_eutils_einfo" name="NCBI EInfo" version="@WRAPPER_VERSION@" profile="@PROFILE@">
  <description>fetch NCBI database metadata</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python einfo.py --version</version_command>
  <command detect_errors="aggressive"><![CDATA[

    python '$__tool_directory__/einfo.py'

    #if $query_type.query_type == 'Description':
      --db $query_type.db_select
    #end if

    @EMAIL_ARGUMENTS@

    > $default

  ]]></command>
  <inputs>
    <conditional name="query_type">
      <param name="query_type" type="select" label="Database Information Request Type" help="List databases or describe a database.">
        <option value="list" selected="True">List available databases</option>
        <option value="Description">Describe a database</option>
      </param>
      <when value="list">
        <param name="db_select" type="hidden" value="Database List"/>
      </when>
      <when value="Description">
        <expand macro="dbselect"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="xml" name="default" label="NCBI Database Information: $query_type.db_select"/>
  </outputs>
  <tests>
    <test>
      <param name="query_type" value="Description"/>
      <param name="db_select" value="pubmed"/>
      <output name="default" file="pubmed.metadata.xml" compare="re_match_multiline" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="query_type" value="list"/>
      <param name="db_select" value="Database list"/>
      <output name="default" ftype="xml">
        <assert_contents>
          <has_text text="&lt;DbName&gt;pubmed&lt;/DbName&gt;"/>
          <is_valid_xml/>
        </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.

@REFERENCES@

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