| Previous changeset 7:bece12dfcf6b (2018-11-05) Next changeset 9:a68a9585241c (2019-01-24) |
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Commit message:
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit f5c5d81fc9781371e12b91c0d609b9201587cda5 |
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modified:
chado.py feature_load_featureprops.xml macros.xml |
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| diff -r bece12dfcf6b -r 402032cb55a1 chado.py --- a/chado.py Mon Nov 05 12:15:55 2018 -0500 +++ b/chado.py Fri Nov 23 11:08:02 2018 -0500 |
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| @@ -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 |
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| diff -r bece12dfcf6b -r 402032cb55a1 feature_load_featureprops.xml --- a/feature_load_featureprops.xml Mon Nov 05 12:15:55 2018 -0500 +++ b/feature_load_featureprops.xml Fri Nov 23 11:08:02 2018 -0500 |
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| @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool id="feature_load_featureprops" name="Chado load feature properties" 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_featureprops @@ -23,32 +23,26 @@ | jq -S . > $results ]]></command> - <inputs> + <inputs> <!-- arguments --> - <param name="tab_file" label="Tab File" argument="tab_file" type="data" format="tabular" help="Path to the tabular 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" /> - <param name="prop_type" label="Property type" argument="prop_type" type="text" help="Type of the feature property (cvterm will be created if it doesn't exist)" /> + <param name="tab_file" label="Tab File" argument="tab_file" type="data" format="tabular" help="Path to the tabular 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" /> + <param name="prop_type" label="Property type" argument="prop_type" type="text" help="Type of the feature property (cvterm will be created if it doesn't exist)" /> <!-- options --> - <param name="feature_type" label="Feature type" argument="feature_type" type="text" help="Type of the target features in sequence ontology (will speed up loading if specified)" optional="true" /> - <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="feature_type" label="Feature type" argument="--feature_type" type="text" help="Type of the target features in sequence ontology (will speed up loading if specified)" optional="true" /> + <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" /> <expand macro="wait_for"/> - </inputs> - <outputs> - <data format="json" name="results"/> - </outputs> - <help> + </inputs> + <outputs> + <data format="json" name="results"/> + </outputs> + <help> Load feature properties from a tabular file (Column1: feature name or uniquename, Column2: property value) @HELP@ - </help> + </help> </tool> |
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| diff -r bece12dfcf6b -r 402032cb55a1 macros.xml --- a/macros.xml Mon Nov 05 12:15:55 2018 -0500 +++ b/macros.xml Fri Nov 23 11:08:02 2018 -0500 |
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| @@ -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> |