Mercurial > repos > immuneml > immuneml_tools

annotate immuneml_simulate_dataset.xml @ 18:697c2b98a466 draft

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author immuneml
date Thu, 17 Mar 2022 16:38:38 +0000
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1 <tool id="immuneml_simulate_dataset" name="Simulate a synthetic immune receptor or repertoire dataset" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>prod_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
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8
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9 cp "$yaml_input" yaml_copy &&
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10 immune-ml ./yaml_copy ${html_outfile.files_path} --tool DataSimulationTool &&
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12 mv ${html_outfile.files_path}/index.html ${html_outfile} &&
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13 mv ${html_outfile.files_path}/immuneML_output.zip $archive
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14
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
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19 </inputs>
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20 <outputs>
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21 <data format="zip" name="archive" label="Archive: dataset simulation"/>
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22 <data format="immuneml_receptors" name="html_outfile" label="ImmuneML dataset (simulated sequences)"/>
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23 </outputs>
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25
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26 <help><![CDATA[
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27
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28 This Galaxy tool allows you to quickly make a dummy dataset.
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29 The tool generates a SequenceDataset, ReceptorDataset or RepertoireDataset consisting of random CDR3 sequences, which could be used for benchmarking machine learning methods or encodings,
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30 or testing out other functionalities.
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31 The amino acids in the sequences are chosen from a uniform random distribution, and there is no underlying structure in the sequences.
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32
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33 You can control:
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34
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35 - The amount of sequences in the dataset, and in the case of a RepertoireDataset, the amount of repertoires
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37 - The length of the generated sequences
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38
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39 - Labels, which can be used as a target when training ML models
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41 Note that since these labels are randomly assigned, they do not bear any meaning and it is not possible to train a ML model with high classification accuracy on this data.
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42 Meaningful labels can be added using the `Simulate immune events into existing repertoire/receptor dataset <root?tool_id=immuneml_simulation>`_ Galaxy tool.
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44 For the exhaustive documentation of this tool and an example YAML specification, see the tutorial `How to simulate an AIRR dataset in Galaxy <https://docs.immuneml.uio.no/latest/galaxy/galaxy_simulate_dataset.html>`_.
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46 **Tool output**
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47
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48 This Galaxy tool will produce the following history elements:
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50 - ImmuneML dataset (simulated sequences): a sequence, receptor or repertoire dataset which can be used as an input to other immuneML tools. The history element contains a summary HTML page describing general characteristics of the dataset, including the name of the dataset
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51 (which is used in the dataset definition of a yaml specification), the dataset type and size, available labels, and a link to download the raw data files.
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53 - Archive: dataset simulation: a .zip file containing the complete output folder as it was produced by immuneML. This folder
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54 contains the output of the DatasetExport instruction including raw data files.
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55 Furthermore, the folder contains the complete YAML specification file for the immuneML run, the HTML output and a log file.
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58 ]]>
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59 </help>
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60
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61 </tool>