--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/esearch.xml	Tue Mar 22 22:30:57 2022 +0000
@@ -0,0 +1,421 @@
+<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>