diff efetch.xml @ 3:c09fcbe4b16a draft

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

--- a/efetch.xml	Wed Mar 11 04:03:36 2020 -0400
+++ b/efetch.xml	Wed Sep 23 09:48:53 2020 +0000
@@ -7,23 +7,21 @@
   <expand macro="requirements"/>
   <version_command>python efetch.py --version</version_command>
   <command detect_errors="aggressive"><![CDATA[
-python '$__tool_directory__/efetch.py'
-$db.db_select
 
-@LIST_OR_HIST@
+    python '$__tool_directory__/efetch.py'
+
+    $db.db_select
 
-#set rettype, retmode = str($db.output_format).split('-')
-## Otherwise, defaults to a None/empty which implies 'default' to NCBI
-#if retmode != "null":
---retmode $retmode
-#end if
---rettype $rettype
+    @LIST_OR_HIST@
 
-@EMAIL_ARGUMENTS@
+    @EMAIL_ARGUMENTS@
+
+    @EFETCH_FORMAT_TOKEN@
+
 ]]></command>
   <inputs>
-    <expand macro="db"/>
     <expand macro="list_or_hist"/>
+    <expand macro="efetchdb"/>
   </inputs>
   <outputs>
     <collection name="output1" type="list" label="NCBI EFetch results">
@@ -33,11 +31,20 @@
   <tests>
     <test>
       <param name="db_select" value="taxonomy"/>
-      <param name="output_format" value="full-xml"/>
+      <param name="output_format" value="none-xml-xml"/>
       <param name="qss" value="id_list"/>
       <param name="id_list" value="10239"/>
       <output_collection name="output1" type="list" count="1">
-        <element name="EFetch Results Chunk 0" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
+        <element name="EFetch-None-xml-chunk1" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
+      </output_collection>
+    </test>
+    <test>
+      <param name="db_select" value="nuccore"/>
+      <param name="output_format" value="fasta-text-fasta"/>
+      <param name="qss" value="id_file"/>
+      <param name="id_file" value="efetchin.tabular"/>
+      <output_collection name="output1" type="list" count="1">
+        <element name="EFetch-fasta-text-chunk1" ftype="xml" file="efetch.tabin.fasta" />
       </output_collection>
     </test>
   </tests>