Mercurial > repos > immuneml > immuneml_tools
comparison immuneml_create_dataset.xml @ 6:2d3dd9ff7e84 draft
"planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
| author | immuneml |
|---|---|
| date | Tue, 27 Jul 2021 09:30:50 +0000 |
| parents | ed3932e6d616 |
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| 5:48569213d91c | 6:2d3dd9ff7e84 |
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| 148 These datasets are in an optimized binary (Pickle) format, which ensures that you can quickly import the dataset into | 148 These datasets are in an optimized binary (Pickle) format, which ensures that you can quickly import the dataset into |
| 149 Galaxy tools without having to repeatedly specify the import parameters. | 149 Galaxy tools without having to repeatedly specify the import parameters. |
| 150 | 150 |
| 151 Before creating a dataset, the relevant data files must first be uploaded to the Galaxy interface. This can be done either | 151 Before creating a dataset, the relevant data files must first be uploaded to the Galaxy interface. This can be done either |
| 152 by uploading files from your local computer (use the 'Upload file' tool under the 'Get local data' menu), or by fetching | 152 by uploading files from your local computer (use the 'Upload file' tool under the 'Get local data' menu), or by fetching |
| 153 remote data from the iReceptor Plus Gateway or VDJdb (see `How to import remote AIRR datasets in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_import_remote_data.html>`_). | 153 remote data from the iReceptor Plus Gateway or VDJdb (see `How to import remote AIRR datasets in Galaxy <https://docs.immuneml.uio.no/latest/galaxy/galaxy_import_remote_data.html>`_). |
| 154 | 154 |
| 155 The imported immuneML dataset is stored in a Galaxy collection, which will appear as a history item on the right side of the screen, | 155 The imported immuneML dataset is stored in a Galaxy collection, which will appear as a history item on the right side of the screen, |
| 156 and can later be selected as input to other tools. | 156 and can later be selected as input to other tools. |
| 157 | 157 |
| 158 The tool has a simplified and an advanced interface. The simplified interface is fully button-based, and relies | 158 The tool has a simplified and an advanced interface. The simplified interface is fully button-based, and relies |
| 159 on default settings for importing datasets. The advanced interface gives full control over import settings through a YAML | 159 on default settings for importing datasets. The advanced interface gives full control over import settings through a YAML |
| 160 specification. In most cases, the simplified interface will suffice. | 160 specification. In most cases, the simplified interface will suffice. |
| 161 | 161 |
| 162 For the exhaustive documentation of this tool and more information about immuneML datasets, see the tutorial `How to make an immuneML dataset in Galaxy <https://docs.immuneml.uio.no/galaxy/galaxy_dataset.html>`_. | 162 For the exhaustive documentation of this tool and more information about immuneML datasets, see the tutorial `How to make an immuneML dataset in Galaxy <https://docs.immuneml.uio.no/latest/galaxy/galaxy_dataset.html>`_. |
| 163 | 163 |
| 164 **Tool output** | 164 **Tool output** |
| 165 | 165 |
| 166 This Galaxy tool will produce the following history elements: | 166 This Galaxy tool will produce the following history elements: |
| 167 | 167 |