diff esummary.xml @ 3:254f40d3ae2b draft

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

--- a/esummary.xml	Wed Mar 11 04:01:46 2020 -0400
+++ b/esummary.xml	Wed Sep 23 09:50:11 2020 +0000
@@ -6,27 +6,66 @@
   </macros>
   <expand macro="requirements"/>
   <version_command>python esummary.py --version</version_command>
-  <command detect_errors="aggressive"><![CDATA[
-python '$__tool_directory__/esummary.py'
-$db_select
+  <command detect_errors="aggressive">
+    <![CDATA[
+
+      python '$__tool_directory__/esummary.py'
+
+      $db_select
+
+      @LIST_OR_HIST@
 
-@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
 
-@EMAIL_ARGUMENTS@
-> $default]]></command>
+      > $default
+
+    ]]>
+  </command>
   <inputs>
+    <expand macro="list_or_hist"/>
     <expand macro="dbselect"/>
-    <expand macro="list_or_hist"/>
+    <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"/>
+    <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>