Mercurial > repos > gga > chado_feature_load_go

changeset 2:602218d4eef5 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 11:11:53 -0500
parents bc1940bf58f2
children eb73aabf7641
files chado.py feature_load_go.xml macros.xml
diffstat 3 files changed, 26 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/chado.py	Mon Nov 05 12:17:48 2018 -0500
+++ b/chado.py	Fri Nov 23 11:11:53 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_go.xml	Mon Nov 05 12:17:48 2018 -0500
+++ b/feature_load_go.xml	Fri Nov 23 11:11:53 2018 -0500
@@ -2,7 +2,7 @@
 <tool id="feature_load_go" name="Chado load GO annotation" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
-    	 <import>macros.xml</import>
+        <import>macros.xml</import>
     </macros>
     <code file="chado.py"/>
     <expand macro="requirements"/>
@@ -29,35 +29,35 @@
 
  > $results
     ]]></command>
-  	<inputs>
-          <!-- arguments -->
-      	<param name="input" label="GO annotation" argument="input" type="data" format="tabular" help="Path to the GO annotation file to load" />
-      	<param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" />
-    	<param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
+    <inputs>
+        <!-- arguments -->
+        <param name="input" label="GO annotation" argument="input" type="data" format="tabular" help="Path to the GO annotation file to load" />
+        <param argument="analysis_id" type="select" dynamic_options="list_analyses()"  label="Analysis" />
+        <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
 
         <!-- options -->
-        <param name="query_type" label="Query type" argument="query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />
+        <param name="query_type" label="Query type" argument="--query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />
 
-    	<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="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="name_column" label="Identifier column" argument="name_column" type="integer" value="2" help="Column containing the feature identifiers." />
+        <param name="name_column" label="Identifier column" argument="--name_column" type="integer" value="2" help="Column containing the feature identifiers." />
 
-    	<param name="go_column" label="GO column" argument="go_column" type="integer" value="5" help="Column containing the GO id." />
+        <param name="go_column" label="GO column" argument="--go_column" type="integer" value="5" help="Column containing the GO id." />
 
-    	<param name="re_name" label="Name regular expression" argument="re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
+        <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
             <expand macro="sanitized"/>
         </param>
 
-    	<param name="skip_missing" label="Skip Missing" argument="skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features or GO id instead of aborting everything." />
+        <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features or GO id instead of aborting everything." />
 
         <expand macro="wait_for"/>
-  	</inputs>
-  	<outputs>
-  		  <data format="txt" name="results"/>
-  	</outputs>
-  	<help>
+    </inputs>
+    <outputs>
+        <data format="txt" name="results"/>
+    </outputs>
+    <help>
 Load GO annotation from a tabular file
 
 @HELP@
-  	</help>
+    </help>
 </tool>
--- a/macros.xml	Mon Nov 05 12:17:48 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:11:53 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>