changeset 2:8b1250de656a 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 12:17:25 2018 -0500
+++ b/chado.py	Fri Nov 23 11:11:02 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/expression_delete_biomaterials.xml	Mon Nov 05 12:17:25 2018 -0500
+++ b/expression_delete_biomaterials.xml	Fri Nov 23 11:11:02 2018 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool id="expression_delete_biomaterials" name="Chado biomaterials delete" 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 expression delete_biomaterials
@@ -25,21 +25,21 @@
 #end if
  > $results
     ]]></command>
-	<inputs>
-	    <!-- options -->
-		<param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
-		<param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" optional="true" />
-		<param name="names" label="Names" argument="names" type="data" format="json" help="JSON list of biomaterial names to delete." optional="true" />
-		<param name="ids" label="Ids" argument="ids" type="data" format="json" help="JSON list of biomaterial ids to delete." optional="true" />
+    <inputs>
+        <!-- options -->
+        <param argument="--organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
+        <param argument="--analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" optional="true" />
+        <param name="names" label="Names" argument="--names" type="data" format="json" help="JSON list of biomaterial names to delete." optional="true" />
+        <param name="ids" label="Ids" argument="--ids" type="data" format="json" help="JSON list of biomaterial ids to delete." optional="true" />
 
-		<expand macro="wait_for"/>
-	</inputs>
-	<outputs>
-		<data format="txt" name="results"/>
-	</outputs>
-	<help>
+        <expand macro="wait_for"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="results"/>
+    </outputs>
+    <help>
 Will delete biomaterials based on selector. Only one selector will be used.
 
 @HELP@
-	</help>
+    </help>
 </tool>

--- a/macros.xml	Mon Nov 05 12:17:25 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:11:02 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>