Mercurial > repos > gga > apollo_feat_from_gff3

diff create_features_from_gff3.xml @ 10:5d1cf95ade8a draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:51:05 -0500
parents 09dacc7c6a21
children bb562d95b6cd
line wrap: on
line diff
--- a/create_features_from_gff3.xml	Mon Jul 29 10:11:02 2019 -0400
+++ b/create_features_from_gff3.xml	Mon Dec 02 05:51:05 2019 -0500
@@ -7,15 +7,16 @@
   <expand macro="requirements"/>
   <code file="webapollo.py"/>
   <command detect_errors="aggressive"><![CDATA[
-python $__tool_directory__/create_features_from_gff3.py
-@ADMIN_AUTH@
+@AUTH@
+
+python '$__tool_directory__/create_features_from_gff3.py'
 @ORG_OR_GUESS@
 
-"$__user_email__"
+'$__user_email__'
 '$gff3_data'
---source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($gff3_data.history_id)}"
+--source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}'
 
-> $output]]></command>
+> '$output']]></command>
   <inputs>
     <expand macro="org_or_guess" />
     <expand macro="gff3_input" />
@@ -26,13 +27,13 @@
     </data>
   </outputs>
   <tests>
-      <test expect_failure="true">
+      <test>
           <conditional name="org_source">
               <param name="source_select" value="direct"/>
               <param name="org_raw" value="Test org" />
           </conditional>
-          <param name="gff3_data" value="good-model.gff3"/>
-          <expand macro="test_result" />
+          <param name="gff3_data" value="merlin.gff"/>
+          <output name="output" file="load_gff3/output.tsv" compare="sim_size"/>
       </test>
   </tests>
   <help><![CDATA[