Mercurial > repos > gga > chado_analysis_add_analysis

changeset 7:72cabf21ce8d 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 11:17:19 -0500
parents 839c51972bb9
children 56689b464826
files analysis_add_analysis.xml chado.py macros.xml
diffstat 3 files changed, 32 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/analysis_add_analysis.xml	Mon Nov 05 12:21:00 2018 -0500
+++ b/analysis_add_analysis.xml	Fri Nov 23 11:17:19 2018 -0500
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <tool id="analysis_add_analysis" name="Chado analysis add" version="@WRAPPER_VERSION@.0">
- <description></description>
-	<macros>
-		<import>macros.xml</import>
-	</macros>
-	<expand macro="requirements"/>
-	<command detect_errors="aggressive"><![CDATA[
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
 @AUTH@
 
 chakin analysis add_analysis
@@ -32,29 +32,29 @@
 
 | jq -S . > $results
     ]]></command>
-	<inputs>
+    <inputs>
     <!-- arguments -->
-	<param name="name" label="Name" argument="name" type="text" help="analysis name" />
-	<param name="program" label="Program" argument="program" type="text" help="analysis program" />
-	<param name="programversion" label="Programversion" argument="programversion" type="text" help="analysis programversion" />
-	<param name="sourcename" label="Sourcename" argument="sourcename" type="text" help="analysis sourcename" />
+    <param name="name" label="Name" argument="name" type="text" help="analysis name" />
+    <param name="program" label="Program" argument="program" type="text" help="analysis program" />
+    <param name="programversion" label="Programversion" argument="programversion" type="text" help="analysis programversion" />
+    <param name="sourcename" label="Sourcename" argument="sourcename" type="text" help="analysis sourcename" />
 
     <!-- options -->
-	<param name="algorithm" label="Algorithm" argument="algorithm" type="text" help="analysis algorithm" optional="True" />
-	<param name="sourceversion" label="Sourceversion" argument="sourceversion" type="text" help="analysis sourceversion" optional="True" />
-	<param name="sourceuri" label="Sourceuri" argument="sourceuri" type="text" help="analysis sourceuri" optional="True" />
-	<param name="description" label="Description" argument="description" type="text" help="analysis description" optional="True" />
-	<param name="date_executed" label="Date Executed" argument="date_executed" type="text" optional="True" help="analysis date_executed (yyyy-mm-dd)">
-		<validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
-	</param>
+    <param name="algorithm" label="Algorithm" argument="--algorithm" type="text" help="analysis algorithm" optional="True" />
+    <param name="sourceversion" label="Sourceversion" argument="--sourceversion" type="text" help="analysis sourceversion" optional="True" />
+    <param name="sourceuri" label="Sourceuri" argument="--sourceuri" type="text" help="analysis sourceuri" optional="True" />
+    <param name="description" label="Description" argument="--description" type="text" help="analysis description" optional="True" />
+    <param name="date_executed" label="Date Executed" argument="--date_executed" type="text" optional="True" help="analysis date_executed (yyyy-mm-dd)">
+        <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
+    </param>
 
-	</inputs>
-	<outputs>
-		<data format="json" name="results"/>
-	</outputs>
-	<help>
+    </inputs>
+    <outputs>
+        <data format="json" name="results"/>
+    </outputs>
+    <help>
 Create an analysis
 
 @HELP@
-	</help>
+    </help>
 </tool>
--- a/chado.py	Mon Nov 05 12:21:00 2018 -0500
+++ b/chado.py	Fri Nov 23 11:17:19 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 12:21:00 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:17:19 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>