diff create_or_update_organism.xml @ 7:cfeab429f660 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a

--- a/create_or_update_organism.xml	Tue Oct 30 04:29:26 2018 -0400
+++ b/create_or_update_organism.xml	Fri Mar 15 06:04:22 2019 -0400
@@ -1,15 +1,14 @@
 <?xml version="1.0"?>
-<tool id="create_or_update" name="Create or Update Organism" version="3.3">
+<tool id="create_or_update" name="Create or Update Organism" version="3.4">
   <description>will create the organism if it doesn't exist, and update otherwise</description>
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements">
+    <requirement type="package" version="377">ucsc-fatotwobit</requirement>
+  </expand>
   <code file="webapollo.py"/>
   <command detect_errors="aggressive"><![CDATA[
-cp -R '${jbrowse.extra_files_path}/data/' "@DATA_DIR@/${jbrowse.id}"
-
-&&
 
 python $__tool_directory__/create_or_update_organism.py
 
@@ -20,11 +19,14 @@
 #if str($group) != "None":
 --group '${group}'
 #end if
+
 ${remove_old_directory}
 $public
 
 @ORG_OR_GUESS@
 
+'${jbrowse.extra_files_path}/data/'
+
 "@DATA_DIR@/${jbrowse.id}"
 
 $__user_email__