| Previous changeset 6:839c51972bb9 (2018-11-05) Next changeset 8:56689b464826 (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:
analysis_add_analysis.xml chado.py macros.xml |
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| diff -r 839c51972bb9 -r 72cabf21ce8d analysis_add_analysis.xml --- 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 |
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| @@ -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> |
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| diff -r 839c51972bb9 -r 72cabf21ce8d chado.py --- a/chado.py Mon Nov 05 12:21:00 2018 -0500 +++ b/chado.py Fri Nov 23 11:17:19 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 839c51972bb9 -r 72cabf21ce8d macros.xml --- a/macros.xml Mon Nov 05 12:21:00 2018 -0500 +++ b/macros.xml Fri Nov 23 11:17:19 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> |