changeset 8:402032cb55a1 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5

--- a/chado.py	Mon Nov 05 12:15:55 2018 -0500
+++ b/chado.py	Fri Nov 23 11:08:02 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/feature_load_featureprops.xml	Mon Nov 05 12:15:55 2018 -0500
+++ b/feature_load_featureprops.xml	Fri Nov 23 11:08:02 2018 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool id="feature_load_featureprops" name="Chado load feature properties" version="@WRAPPER_VERSION@.0">
- <description></description>
-	<macros>
-		<import>macros.xml</import>
-	</macros>
-	<expand macro="requirements"/>
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
     <code file="chado.py"/>
-	<command detect_errors="aggressive"><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
 @AUTH@
 
 chakin feature load_featureprops
@@ -23,32 +23,26 @@
 
 | jq -S . > $results
     ]]></command>
-	<inputs>
+    <inputs>
         <!-- arguments -->
-    	<param name="tab_file" label="Tab File" argument="tab_file" type="data" format="tabular" help="Path to the tabular file to load" />
-    	<param argument="--analysis_id"
-    		type="select"
-    		dynamic_options="list_analyses()"
-    		label="Analysis" />
-        <param argument="--organism"
-               type="select"
-               dynamic_options="list_organisms()"
-               label="Organism" />
-    	<param name="prop_type" label="Property type" argument="prop_type" type="text" help="Type of the feature property (cvterm will be created if it doesn't exist)" />
+        <param name="tab_file" label="Tab File" argument="tab_file" type="data" format="tabular" help="Path to the tabular file to load" />
+        <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
+        <param argument="organism" type="select" dynamic_options="list_organisms()" label="Organism" />
+        <param name="prop_type" label="Property type" argument="prop_type" type="text" help="Type of the feature property (cvterm will be created if it doesn't exist)" />
 
         <!-- options -->
-    	<param name="feature_type" label="Feature type" argument="feature_type" type="text" help="Type of the target features in sequence ontology (will speed up loading if specified)" optional="true" />
-    	<param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
+        <param name="feature_type" label="Feature type" argument="--feature_type" type="text" help="Type of the target features in sequence ontology (will speed up loading if specified)" optional="true" />
+        <param name="match_on_name" label="Match on name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
 
         <expand macro="wait_for"/>
 
-	</inputs>
-	<outputs>
-		<data format="json" name="results"/>
-	</outputs>
-	<help>
+    </inputs>
+    <outputs>
+        <data format="json" name="results"/>
+    </outputs>
+    <help>
 Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value)
 
 @HELP@
-	</help>
+    </help>
 </tool>

--- a/macros.xml	Mon Nov 05 12:15:55 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:08:02 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>