| Previous changeset 1:4843796fcbf6 (2019-03-05) |
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Commit message:
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1" |
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modified:
expression_add_biomaterial.xml macros.xml |
| b |
| diff -r 4843796fcbf6 -r 5e02721168e9 expression_add_biomaterial.xml --- a/expression_add_biomaterial.xml Tue Mar 05 05:24:55 2019 -0500 +++ b/expression_add_biomaterial.xml Wed Aug 14 10:02:37 2019 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.0"> +<tool id="expression_add_biomaterial" name="Create a biomaterial" version="@WRAPPER_VERSION@.1"> <description>in Tripal</description> <macros> <import>macros.xml</import> @@ -30,6 +30,8 @@ <!-- arguments --> <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" /> <param name="file_path" label="Biomaterial description sheet" argument="file_path" type="data" format="xml,tsv,csv" help="A file describing the biomaterial" /> + + <expand macro="wait_for"/> </inputs> <outputs> <data format="txt" name="results"/> |
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| diff -r 4843796fcbf6 -r 5e02721168e9 macros.xml --- a/macros.xml Tue Mar 05 05:24:55 2019 -0500 +++ b/macros.xml Wed Aug 14 10:02:37 2019 -0400 |
| [ |
| @@ -41,13 +41,15 @@ <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token> <token name="@AUTH@"><![CDATA[ - echo "__default: local" > '.auth.yml' && - echo "local:" >> '.auth.yml' && - echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' && - echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' && - echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' && + if [ -z "\$TRIPAILLE_GLOBAL_CONFIG_PATH" ]; then + echo "__default: local" > '.auth.yml' && + echo "local:" >> '.auth.yml' && + echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' && + echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' && + echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' && - TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml' + export TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml' + ; fi && ]]></token> <xml name="wait_for"> @@ -155,7 +157,7 @@ <section name="matching" title="Feature matching" expanded="True"> <param name="query_type" type="text" - label="The feature type of the blast query" + label="The feature type of the query" help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" /> <param name="query_uniquename" @@ -163,13 +165,13 @@ checked="false" truevalue="--query_uniquename" falsevalue="" - label="Find blast query features using their Unique name" + label="Find query features using their Unique name" help="Feature name will be used otherwise" /> <param name="query_re" type="text" optional="true" - label="Regular expression to extract the feature name from the blast query name" + label="Regular expression to extract the feature name from the query name" help="leave empty if the first word in query name is sufficient"> <expand macro="sanitized"/> </param> |