view esearch.xml @ 0:c8a84e910e6b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db

<?xml version="1.0"?>
<tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@">
  <description>search NCBI Databases by text query</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python esearch.py --version</version_command>
  <command detect_errors="aggressive" interpreter="python"><![CDATA[esearch.py
$db_select
"$term"

#if $history_file and $history_file is not None:
    --history_file $history_file
#end if

#if $date.enabled:
    --datetype $date.datetype

    #if $date.reldate and $date.reldate is not None:
    --reldate $date.reldate
    #end if

    #if $date.mindate and $date.mindate is not None:
    --mindate $date.mindate
    #end if

    #if $date.maxdate and $date.maxdate is not None:
    --maxdate $date.maxdate
    #end if
#end if

#if $use_history:
    --history_out $history
#end if

@EMAIL_ARGUMENTS@
> $default]]></command>
  <inputs>
    <expand macro="dbselect"/>
    <param label="Search Term" name="term" type="text">
      <sanitizer>
        <valid>
          <add value="'"/>
          <add value="["/>
          <add value="]"/>
        </valid>
      </sanitizer>
    </param>
    <param label="Filter existing history" name="history_file" type="data" format="json" optional="True"/>
    <param checked="false" label="Store results to history server" name="use_history" type="boolean" truevalue="--use_history" falsevalue=""/>
    <conditional name="date">
      <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="enabled"/>
      <when value="True">
        <param label="Date type" name="datetype" type="select">
          <option value="PDAT">Publish Date</option>
          <option value="EDAT">Entrez Date</option>
          <option value="MDAT">Modification Date</option>
        </param>
        <param label="In past N days" name="reldate" type="integer" min="1" optional="True"/>
        <param label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="mindate" type="text"/>
        <param label="maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="maxdate" type="text"/>
      </when>
      <when value="False"/>
    </conditional>
  </inputs>
  <outputs>
    <data format="json" name="default" label="ESearch Results for $term">
      <change_format>
        <when input="use_history" value="" format="xml"/>
      </change_format>
    </data>
    <expand macro="history_out">
      <filter>use_history</filter>
    </expand>
  </outputs>
  <tests>
    <test>
      <param name="db_select" value="pubmed"/>
      <param name="term" value="(PNAS[ta] AND 97[vi])"/>
      <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
    </test>
    <test>
      <param name="db_select" value="pubmed"/>
      <param name="term" value="PNAS[ta]"/>
      <param name="enabled" value="True"/>
      <param name="datetype" value="PDAT"/>
      <param name="mindate" value="2014/01/01"/>
      <param name="maxdate" value="2014/02/01"/>
      <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
    </test>
  </tests>
  <help><![CDATA[
NCBI Entrez ESearch
===================

Responds to a text query with the list of matching UIDs in a given database
(for later use in ESummary, EFetch or ELink), along with the term translations
of the query.

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

Search in PubMed with the term cancer for abstracts that have an Entrez date
within the last 60 days:

+----------------------+-------------+
| Parameter            | Value       |
+======================+=============+
| NCBI Database to Use | PubMed      |
+----------------------+-------------+
| Term                 | Cancer      |
+----------------------+-------------+
| Datetype             | Entrez Date |
+----------------------+-------------+
| In past N Days       | 60          |
+----------------------+-------------+

Search PubMed Central for free full text articles containing the query stem cells:

+----------------------+--------------------------------------+
| Parameter            | Value                                |
+======================+======================================+
| NCBI Database to Use | PubMedCentral                        |
+----------------------+--------------------------------------+
| Term                 | Stem Cells AND free fulltext[filter] |
+----------------------+--------------------------------------+

Search in Nucleotide for all tRNAs:

+----------------------+--------------------------------------+
| Parameter            | Value                                |
+======================+======================================+
| NCBI Database to Use | Nucleotide                           |
+----------------------+--------------------------------------+
| Term                 | biomol trna[prop]                    |
+----------------------+--------------------------------------+

Search in Protein for a molecular weight range:

+----------------------+--------------------------------------+
| Parameter            | Value                                |
+======================+======================================+
| NCBI Database to Use | Protein                              |
+----------------------+--------------------------------------+
| Term                 | 70000:90000[molecular weight]        |
+----------------------+--------------------------------------+


@REFERENCES@

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