Mercurial > repos > gga > chado_feature_load_fasta

changeset 9:11b65a23c85d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 10:58:00 -0500
parents e2076be814d9
children 965f9824624d
files chado.py feature_load_fasta.xml macros.xml
diffstat 3 files changed, 58 insertions(+), 54 deletions(-) [+]
line wrap: on
line diff
--- a/chado.py	Mon Nov 05 12:09:29 2018 -0500
+++ b/chado.py	Fri Nov 23 10:58:00 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_fasta.xml	Mon Nov 05 12:09:29 2018 -0500
+++ b/feature_load_fasta.xml	Fri Nov 23 10:58:00 2018 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool id="feature_load_fasta" name="Chado load fasta" 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_fasta
@@ -45,57 +45,55 @@
 
 | jq -S . > $results
     ]]></command>
-	<inputs>
-	    <!-- arguments -->
-		<param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" />
-	    <param argument="--organism"
-	           type="select"
-	           dynamic_options="list_organisms()"
-	           label="Organism" />
+    <inputs>
+        <!-- arguments -->
+        <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="Path to the Fasta file to load" />
+        <param argument="--organism" type="select" dynamic_options="list_organisms()" label="Organism" />
 
-	    <!-- options -->
-		<param argument="--analysis_id"
-			type="select"
-			dynamic_options="list_analyses()"
-			label="Analysis" />
-		<param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/>
+        <!-- options -->
+        <param argument="--analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
+        <param name="sequence_type" label="Sequence Type" type="text" value="contig" help="this should be a Sequence Ontology term"/>
 
-		<param name="re_name" label="Name regular expression" argument="re_name" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" />
-		<param name="re_uniquename" label="Uniquename regular expression" argument="re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true" />
-		<param name="match_on_name" label="Match on name" argument="match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" />
-		<param name="do_update" label="Update" argument="update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" />
-	    <conditional name="relationships">
-			<param name="rel_type"
-				   argument="--rel_type"
-				   type="select"
-				   label="Relationship type"
-				   help="Use this when inserting features that should be associated to other already existing features">
-				<option value="none" selected="true">No relationship</option>
-				<option value="part_of">Part of (for CDS sequences)</option>
-				<option value="derives_from">Derives from (for peptide sequences)</option>
-			</param>
-			<when value="none"/>
-			<when value="part_of">
-				<expand macro="feature_rel" />
-			</when>
-			<when value="derives_from">
-				<expand macro="feature_rel" />
-			</when>
-		</conditional>
-	    <section name="ext_db" title="Cross references to external database">
-			<param name="db" label="Db" argument="db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db -->
-			<param name="re_db_accession" label="Regex external db accession" argument="re_db_accession" type="text" help="Regular expression to extract an external database accession from the fasta sequence id (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 fasta sequence id (first capturing group will be used)." optional="true">
+            <expand macro="sanitized"/>
+        </param>
+        <param name="re_uniquename" label="Uniquename regular expression" argument="--re_uniquename" type="text" help="Regular expression to extract the feature name from the fasta sequence id (first capturing group will be used)." optional="true">
+            <expand macro="sanitized"/>
+        </param>
+        <param name="match_on_name" label="Match on name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match existing features using their name instead of their uniquename" />
+        <param name="do_update" label="Update" argument="--update" type="boolean" truevalue="--update" falsevalue="" help="Update existing feature with new sequence instead of throwing an error" />
+        <conditional name="relationships">
+            <param name="rel_type"
+                   argument="--rel_type"
+                   type="select"
+                   label="Relationship type"
+                   help="Use this when inserting features that should be associated to other already existing features">
+                <option value="none" selected="true">No relationship</option>
+                <option value="part_of">Part of (for CDS sequences)</option>
+                <option value="derives_from">Derives from (for peptide sequences)</option>
+            </param>
+            <when value="none"/>
+            <when value="part_of">
+                <expand macro="feature_rel" />
+            </when>
+            <when value="derives_from">
+                <expand macro="feature_rel" />
+            </when>
+        </conditional>
+        <section name="ext_db" title="Cross references to external database">
+            <param name="db" label="Db" argument="--db" type="integer" help="External database to cross reference to." optional="true" /><!-- FIXME get this from db -->
+            <param name="re_db_accession" label="Regex external db accession" argument="--re_db_accession" type="text" help="Regular expression to extract an external database accession from the fasta sequence id (first capturing group will be used)." optional="true">
                 <expand macro="sanitized"/>
             </param>
-	    </section>
-	    <expand macro="wait_for"/>
-	</inputs>
-	<outputs>
-		<data format="json" name="results"/>
-	</outputs>
-	<help>
+        </section>
+        <expand macro="wait_for"/>
+    </inputs>
+    <outputs>
+        <data format="json" name="results"/>
+    </outputs>
+    <help>
 Load features from a fasta file
 
 @HELP@
-	</help>
+    </help>
 </tool>
--- a/macros.xml	Mon Nov 05 12:09:29 2018 -0500
+++ b/macros.xml	Fri Nov 23 10:58:00 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>