| Previous changeset 8:e2076be814d9 (2018-11-05) Next changeset 10:965f9824624d (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_fasta.xml macros.xml |
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| diff -r e2076be814d9 -r 11b65a23c85d chado.py --- a/chado.py Mon Nov 05 12:09:29 2018 -0500 +++ b/chado.py Fri Nov 23 10:58:00 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 e2076be814d9 -r 11b65a23c85d feature_load_fasta.xml --- 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 |
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| @@ -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> |
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| diff -r e2076be814d9 -r 11b65a23c85d macros.xml --- a/macros.xml Mon Nov 05 12:09:29 2018 -0500 +++ b/macros.xml Fri Nov 23 10:58:00 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> |