| Previous changeset 1:8dff71edbce5 (2021-11-18) Next changeset 3:0cadd0a04412 (2021-11-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475" |
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modified:
data_manager/funannotate.py data_manager/funannotate.xml |
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| diff -r 8dff71edbce5 -r 13018941c6a0 data_manager/funannotate.py --- a/data_manager/funannotate.py Thu Nov 18 21:55:43 2021 +0000 +++ b/data_manager/funannotate.py Fri Nov 19 11:15:54 2021 +0000 |
| [ |
| @@ -224,6 +224,7 @@ parser = argparse.ArgumentParser() parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)') + parser.add_argument('--wget', dest='wget', action='store_true', help='Download using wget (instead of urllib)') parser.add_argument("version_id") parser.add_argument("datatable_name") parser.add_argument("galaxy_datamanager_filename") @@ -243,6 +244,8 @@ cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all'] if args.partial: cmd_args += ['-i', 'merops', '-b', 'eukaryota'] + if args.wget: + cmd_args += ['--wget'] proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory) return_code = proc.wait() if return_code: |
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| diff -r 8dff71edbce5 -r 13018941c6a0 data_manager/funannotate.xml --- a/data_manager/funannotate.xml Thu Nov 18 21:55:43 2021 +0000 +++ b/data_manager/funannotate.xml Fri Nov 19 11:15:54 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.2" tool_type="manage_data" profile="20.01"> +<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01"> <requirements> <requirement type="package" version="1.8.9">funannotate</requirement> <requirement type="package" version="2.26.0">requests</requirement> @@ -7,12 +7,14 @@ <command detect_errors="exit_code"><![CDATA[ python -u '$__tool_directory__/funannotate.py' $partial_data +$wget \$(date +'%Y-%m-%d-%H%M%S') 'funannotate' '${output_file}' ]]></command> <inputs> <param name="partial_data" type="hidden" value="" help="Used for testing"/> + <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/> </inputs> <outputs> <data name="output_file" format="data_manager_json"/> @@ -27,6 +29,16 @@ </assert_contents> </output> </test> + <test> + <param name="partial_data" value="--partial"/> + <param name="wget" value="True"/> + <output name="output_file"> + <assert_contents> + <has_text text="Funannotate database "/> + <has_text text='"format_version": "1.0"'/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ This data managers fetches data from various databases for the funannotate |