view esearch.xml @ 0:b6ffd64c448e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"

<tool id="ncbi_entrez_direct_esearch" name="NCBI ESearch" version="@TOOL_VERSION@">
    <description>search NCBI Databases by text query</description>
    <macros>
      <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>esearch -version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        @ECONTACT@
        esearch
        -db "${db.db}"
        -sort "${db.sort}"
        -query "${query}"
        ${spell}
        #if $date.constraint:
            -datetype $date.datetype
            #if str( $date.days ):
                -days "${date.days}"
            #end if
            #if str( $date.mindate ):
                -mindate "${date.mindate}"
            #end if
            #if str( $date.maxdate ):
                -maxdate "${date.maxdate}"
            #end if
        #end if
        > '$output_xml'
  ]]>
  </command>
  <inputs>
    <conditional name="db">
        <param name="db" type="select" label="Choose your DB" argument="-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 value="annotinfo">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="assembly">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="bioproject">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="biosample">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="biosystems">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="blastdbinfo">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="books">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="cdd">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="clinvar">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="clone">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="dbvar">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="gap">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="gapplus">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="gds">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="gencoll">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="gene">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="genome">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="geoprofiles">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="grasp">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="gtr">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="homologene">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="medgen">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="mesh">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="ncbisearch">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="nlmcatalog">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="nuccore">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="nucest">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="nucgss">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="nucleotide">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="omim">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="orgtrack">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="pcassay">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="pccompound">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="pcsubstance">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="pmc">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="popset">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="probe">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="protein">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="proteinclusters">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="pubmed">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="pubmedhealth">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="seqannot">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="snp">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="sra">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="structure">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="taxonomy">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
        <when value="unigene">
            <param name="sort" type="select" label="Sort results by" argument="-sort">
                <option value="Default Order">Default Order</option>
            </param>
        </when>
    </conditional>
    <param label="Search Term" name="query" type="text" argument="-query">
        <sanitizer>
            <valid>
                <add value="'"/>
                <add value="["/>
                <add value="]"/>
            </valid>
        </sanitizer>
    </param>
    <param name="spell" label="Correct misspellings in query" type="boolean" truevalue="-spell" falsevalue="" checked="false"/>
    <conditional name="date">
        <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="constraint"/>
        <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="Number of days in the past" name="days" value="" 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="xml" name="output_xml" label="ESearch Results for $query"/>
  </outputs>
  <tests>
    <test>
      <param name="db" value="sra"/>
      <param name="query" value="SRP000007"/>
      <output name="output_xml">
          <assert_contents>
              <has_text_matching expression="ENTREZ_DIRECT" />
              <has_text_matching expression="sra" />
              <has_text_matching expression="WebEnv" />
              <has_text_matching expression="QueryKey" />
              <has_text_matching expression="Count" />
              <has_text_matching expression="Step" />
              <has_text_matching expression="WebEnv" />
          </assert_contents>
      </output>
    </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]        |
+----------------------+--------------------------------------+

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