Mercurial > repos > iuc > ena_webin_cli

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
author iuc
date Tue, 05 Aug 2025 11:53:57 +0000
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
iuc
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1 Webin CLI wrapper
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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2 ======================
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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3 the submission of genome assemblies using the
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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4 [Webin-cli](https://github.com/enasequence/webin-cli)
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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6 This is a Galaxy wrapper for `webin cli <https://github.com/enasequence/webin-cli>`__ tool from `ENA <https://www.ebi.ac.uk/ena/browser/home>`__.
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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9 Setting up credentials on Galaxy
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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10 --------------------------------
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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12 The admin of the server can set up global credentials through a file
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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13 with the format:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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15 .. code-block:: yaml
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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17 username: webin_id
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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18 password: webin_password
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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20 The path to this file must be exported as an environment variable called
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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21 $GALAXY_ENA_SECRETS
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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23 Alternatively, the admin can enable users to set their own credentials
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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24 for this tool. To enable it, make sure the file
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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25 ``config/user_preferences_extra_conf.yml`` has the following section:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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27 .. code-block:: yaml
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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28
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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29 ena_webin_account:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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30 description: Your ENA Webin account details
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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31 inputs:
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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32 - name: webin_id
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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33 label: ENA Webin ID
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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34 type: text
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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35 required: False
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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36 - name: password
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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37 label: Password
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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38 type: password
c9f87770ba8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli commit 35b4a063e227ea4a2440e23c4df5c27e42c077cb
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39 required: False