diff esearch.xml @ 2:f6046ed1f915 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b
author iuc
date Sat, 18 May 2024 20:23:03 +0000
parents b6ffd64c448e
children
line wrap: on
line diff
--- a/esearch.xml	Sat Dec 17 20:44:51 2022 +0000
+++ b/esearch.xml	Sat May 18 20:23:03 2024 +0000
@@ -1,365 +1,368 @@
 <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>
+        <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 "${query}"
+        -db '${db.db}'
+        -sort '${db.sort}'
+        -query '${query}'
         ${spell}
         #if $date.constraint:
             -datetype $date.datetype
             #if str( $date.days ):
-                -days "${date.days}"
+                -days '${date.days}'
             #end if
             #if str( $date.mindate ):
-                -mindate "${date.mindate}"
+                -mindate '${date.mindate}'
             #end if
             #if str( $date.maxdate ):
-                -maxdate "${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>
+    <inputs>
+        <conditional name="db">
+            <param argument="-db" type="select" label="Choose your 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>
-        <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>
+            <when value="annotinfo">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="assembly">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="bioproject">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="biosample">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="biosystems">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="blastdbinfo">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="books">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="cdd">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="clinvar">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="clone">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="dbvar">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="gap">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="gapplus">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="gds">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="gencoll">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="gene">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="genome">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="geoprofiles">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="grasp">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="gtr">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="homologene">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="medgen">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="mesh">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="ncbisearch">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="nlmcatalog">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="nuccore">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="nucest">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="nucgss">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="nucleotide">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="omim">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="orgtrack">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="pcassay">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="pccompound">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="pcsubstance">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="pmc">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="popset">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="probe">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="protein">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="proteinclusters">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="pubmed">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="pubmedhealth">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="seqannot">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="snp">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="sra">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="structure">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="taxonomy">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+            <when value="unigene">
+                <param argument="-sort" type="select" label="Sort results by">
+                    <option value="Default Order">Default Order</option>
+                </param>
+            </when>
+        </conditional>
+        <param argument="-query" type="text" label="Search Term">
+            <sanitizer>
+                <valid>
+                    <add value="'"/>
+                    <add value="["/>
+                    <add value="]"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="-spell" type="boolean" truevalue="-spell" falsevalue="" checked="false" label="Correct misspellings in query"/>
+        <conditional name="date">
+            <param name="constraint" type="select" label="Filter By Date">
+                <option value="True">Filter by date</option>
+                <option value="False">Don't filter</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[
+            <when value="True">
+                <param name="datetype" type="select" label="Date type">
+                    <option value="PDAT">Publish Date</option>
+                    <option value="EDAT">Entrez Date</option>
+                    <option value="MDAT">Modification Date</option>
+                </param>
+                <param name="days" type="integer" min="1" value="" optional="True" label="Number of days in the past"/>
+                <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD"/>
+                <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD"/>
+            </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
 ===================
 
@@ -417,5 +420,5 @@
 
 @DISCLAIMER@
       ]]></help>
-  <expand macro="citations"/>
+    <expand macro="citations"/>
 </tool>