# HG changeset patch
# User gga
# Date 1542989747 18000
# Node ID 4451447ae06537a9ebaddb09dd4ee0b7e612391c
# Parent  60d7b4054865c358a0a53d2b6458f3b4687dfdcd
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5

diff -r 60d7b4054865 -r 4451447ae065 chado.py
--- a/chado.py	Mon Nov 05 12:20:09 2018 -0500
+++ b/chado.py	Fri Nov 23 11:15:47 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
 
 
diff -r 60d7b4054865 -r 4451447ae065 feature_load_gff.xml
--- a/feature_load_gff.xml	Mon Nov 05 12:20:09 2018 -0500
+++ b/feature_load_gff.xml	Fri Nov 23 11:15:47 2018 -0500
@@ -2,7 +2,7 @@
 <tool id="feature_load_gff" name="Chado load gff" version="@WRAPPER_VERSION@.0">
     <description></description>
     <macros>
-    	 <import>macros.xml</import>
+        <import>macros.xml</import>
     </macros>
     <code file="chado.py"/>
     <expand macro="requirements"/>
@@ -19,15 +19,15 @@
 #end if
 
 #if $prot_naming.method == 'regex'
-    #if $re_protein:
-      --re_protein '$re_protein'
+    #if $prot_naming.re_protein:
+      --re_protein '$prot_naming.re_protein'
     #end if
-    #if $re_protein_capture:
-      --re_protein_capture '$re_protein_capture'
+    #if $prot_naming.re_protein_capture:
+      --re_protein_capture '$prot_naming.re_protein_capture'
     #end if
 #elif $prot_naming.method == "attr"
-    #if $protein_id_attr:
-      --protein_id_attr '$protein_id_attr'
+    #if $prot_naming.protein_id_attr:
+      --protein_id_attr '$prot_naming.protein_id_attr'
     #end if
 #end if
 
@@ -43,20 +43,14 @@
 
  > $results
     ]]></command>
-  	<inputs>
-          <!-- arguments -->
-      	<param name="gff" label="Gff" argument="gff" type="data" format="gff" help="Path to the Fasta 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" />
+    <inputs>
+        <!-- arguments -->
+        <param name="gff" label="Gff" argument="gff" type="data" format="gff" help="Path to the Fasta 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" />
 
-          <!-- options -->
-      	<param name="landmark_type" label="Landmark Type" argument="landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" />
+        <!-- options -->
+        <param name="landmark_type" label="Landmark Type" argument="--landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" />
         <conditional name="prot_naming">
             <param name="method" type="select" label="Protein naming method" help="Will be used to assign uniquename to polypeptide">
                 <option value="auto">Automatic: uses GFF polypeptide features if existing, or derive from mRNA uniquename</option>
@@ -66,30 +60,30 @@
             <when value="auto">
             </when>
             <when value="regex">
-                <param name="re_protein_capture" label="Regex protein capture" argument="re_protein_capture" type="text" help="Regular expression to capture groups in mRNA uniquename to use in 'Regex protein'" value="^(.*?)-R([A-Z]+)$">
+                <param name="re_protein_capture" label="Regex protein capture" argument="--re_protein_capture" type="text" help="Regular expression to capture groups in mRNA uniquename to use in 'Regex protein'" value="^(.*?)-R([A-Z]+)$">
                     <expand macro="sanitized"/>
                 </param>
-              	<param name="re_protein" label="Regex protein" argument="re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture'" value="\1-P\2">
+                  <param name="re_protein" label="Regex protein" argument="--re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture'" value="\1-P\2">
                     <expand macro="sanitized"/>
                 </param>
             </when>
             <when value="attr">
-                <param name="protein_id_attr" label="Protein id attribute" argument="protein_id_attr" type="text" help="Attribute containing the protein uniquename. It is searched at the mRNA level, and if not found at CDS level." value="protein_id"/>
+                <param name="protein_id_attr" label="Protein id attribute" argument="--protein_id_attr" type="text" help="Attribute containing the protein uniquename. It is searched at the mRNA level, and if not found at CDS level." value="protein_id"/>
             </when>
         </conditional>
 
-      	<param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" />
-      	<param name="no_seq_compute" label="Allow computing missing sequences" argument="no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." />
-      	<param name="add_only" label="Add only" argument="add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." />
+        <param name="fasta" label="Fasta" argument="--fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" />
+        <param name="no_seq_compute" label="Allow computing missing sequences" argument="--no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." />
+        <param name="add_only" label="Add only" argument="--add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." />
 
         <expand macro="wait_for"/>
-  	</inputs>
-  	<outputs>
-  		  <data format="txt" name="results"/>
-  	</outputs>
-  	<help>
+    </inputs>
+    <outputs>
+        <data format="txt" name="results"/>
+    </outputs>
+    <help>
 Load features from a gff file
 
 @HELP@
-  	</help>
+    </help>
 </tool>
diff -r 60d7b4054865 -r 4451447ae065 macros.xml
--- a/macros.xml	Mon Nov 05 12:20:09 2018 -0500
+++ b/macros.xml	Fri Nov 23 11:15:47 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>