Mercurial > repos > gga > chado_phylogeny_gene_families

changeset 8:9867cab3574b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5
author gga
date Fri, 23 Nov 2018 11:13:19 -0500
parents 56ffe836585b
children b08a3baff107
files chado.py macros.xml phylogeny_gene_families.xml
diffstat 3 files changed, 10 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/chado.py	Mon Nov 05 12:18:28 2018 -0500
+++ b/chado.py	Fri Nov 23 11:13:19 2018 -0500
@@ -406,6 +406,7 @@
         # there.
         data = _list_organisms(ci, *args, **kwargs)
         cache[cacheKey] = data
+        ci.session.close()
         return data
     try:
         # The cache key may or may not be in the cache at this point, it
@@ -413,12 +414,14 @@
         # when we checked above and now, so we reference the object from the
         # cache in preparation to return.
         data = cache[cacheKey]
+        ci.session.close()
         return data
     except KeyError:
         # If access fails due to eviction, we will fail over and can ensure that
         # data is inserted.
         data = _list_organisms(ci, *args, **kwargs)
         cache[cacheKey] = data
+        ci.session.close()
         return data
 
 
@@ -447,6 +450,7 @@
 
         data = _list_analyses(ci, *args, **kwargs)
         cache[cacheKey] = data
+        ci.session.close()
         return data
     try:
         # The cache key may or may not be in the cache at this point, it
@@ -454,12 +458,14 @@
         # when we checked above and now, so we reference the object from the
         # cache in preparation to return.
         data = cache[cacheKey]
+        ci.session.close()
         return data
     except KeyError:
         # If access fails due to eviction, we will fail over and can ensure that
         # data is inserted.
         data = _list_analyses(ci, *args, **kwargs)
         cache[cacheKey] = data
+        ci.session.close()
         return data
 
 
--- a/macros.xml	Mon Nov 05 12:18:28 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:13:19 2018 -0500
@@ -2,7 +2,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.2.2">python-chado</requirement>
+            <requirement type="package" version="2.2.3">python-chado</requirement>
             <requirement type="package" version="1.5">jq</requirement>
             <yield/>
         </requirements>
@@ -16,7 +16,7 @@
         </stdio>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.2.2</token>
+    <token name="@WRAPPER_VERSION@">2.2.3</token>
 
     <xml name="citation">
         <citations>
--- a/phylogeny_gene_families.xml	Mon Nov 05 12:18:28 2018 -0500
+++ b/phylogeny_gene_families.xml	Fri Nov 23 11:13:19 2018 -0500
@@ -20,8 +20,8 @@
     ]]></command>
 	<inputs>
         <!-- options -->
-    	<param name="family_name" label="Family Name" argument="family_name" type="text" help="Restrict to families beginning with given prefix" />
-    	<param name="nuke" label="Nuke" argument="nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene families data" />
+    	<param name="family_name" label="Family Name" argument="--family_name" type="text" help="Restrict to families beginning with given prefix" />
+    	<param name="nuke" label="Nuke" argument="--nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene families data" />
         <expand macro="wait_for"/>
 
 	</inputs>