view esummary.xml @ 3:254f40d3ae2b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"

<?xml version="1.0"?>
<tool id="ncbi_eutils_esummary" name="NCBI ESummary" version="@WRAPPER_VERSION@" profile="@PROFILE@">
  <description>fetch summary of history/ids</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python esummary.py --version</version_command>
  <command detect_errors="aggressive">
    <![CDATA[

      python '$__tool_directory__/esummary.py'

      $db_select

      @LIST_OR_HIST@

      @EMAIL_ARGUMENTS@

      #if $retstart is not None:
        --retstart '$retstart'
      #end if

      #if $retmax is not None:
        --retmax '$retmax'
      #end if

      #if $output_format == 'xml':
        --retmode xml
      #elif $output_format == 'json':
        --retmode json
      #end if

      > $default

    ]]>
  </command>
  <inputs>
    <expand macro="list_or_hist"/>
    <expand macro="dbselect"/>
    <param name="retstart" type="integer" value="0" min="0" max="99999" label="Starting record to return (--retstart)" />
    <param name="retmax" type="integer" value="100000" min="1" max="100000" label="Maximum number of records to return (--retmax)" />
    <param name="output_format" type="select" label="Output Format">
      <option value="xml" selected="True">XML</option>
      <option value="json">JSON</option>
    </param>
  </inputs>
  <outputs>
    <data format="xml" name="default" label="Summary of NCBI Search">
      <change_format>
        <when input="output_format" value="xml" format="xml" />
        <when input="output_format" value="json" format="json" />
      </change_format>
      <filter>query_source['qss'] != 'history_json' and query_source['qss'] != 'history_xml'</filter>
    </data>
    <collection name="summaries" type="list" label="Summary of NCBI Searches">
      <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
      <filter>query_source['qss'] == 'history_json' or query_source['qss'] == 'history_xml'</filter>
    </collection>
  </outputs>
  <tests>
    <test>
      <param name="qss" value="id_list"/>
      <param name="id_list" value="10239"/>
      <param name="db_select" value="taxonomy"/>
      <param name="retstart" value="0"/>
      <param name="retmax" value="100000"/>
      <param name="output_format" value="xml"/>
      <output name="default" file="esummary.tax.xml" ftype="xml"/>
    </test>
  </tests>
  <help><![CDATA[
NCBI Entrez ESummary
====================

Responds to a list of UIDs from a given database with the corresponding
document summaries.

Example Queries
---------------

Search against protein:

+----------------------+--------------------------------------+
| Parameter            | Value                                |
+======================+======================================+
| NCBI Database to Use | Protein                              |
+----------------------+--------------------------------------+
| ID List              | 28800982 28628843                    |
+----------------------+--------------------------------------+

@REFERENCES@

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