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annotate immuneml_simulate_events.xml @ 15:e33b3d370124 draft

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"planemo upload commit 5d2abc4e7c3895a90cefc6384e0964049e9bcb9f"
author immuneml
date Tue, 04 Jan 2022 12:57:42 +0000
parents 45ca02982e1f
children cd57c1c66f8b
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1 <tool id="immuneml_simulation" name="Simulate immune events into an existing 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 #if $iml_input
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10 cp -r ${iml_input.extra_files_path}/result/* . &&
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11 (mv repertoires/* . &>/dev/null || :) &&
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12 rm -rf repertoires &&
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13 #end if
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15 cp "$yaml_input" yaml_copy &&
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16 immune-ml ./yaml_copy ${html_outfile.files_path} --tool GalaxySimulationTool &&
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18 mv ${html_outfile.files_path}/index.html ${html_outfile} &&
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19 mv ${html_outfile.files_path}/immuneML_output.zip $archive
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20
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="iml_input" type="data" format="immuneml_receptors" label="Dataset input" optional="true" help="This field accepts datasets ithe ImmuneML format, as created by the Create Dataset tool."/>
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25 <param name="yaml_input" type="data" format="txt" label="YAML specification" multiple="false"/>
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26 </inputs>
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27 <outputs>
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28 <data format="zip" name="archive" label="Archive: immune signal simulation"/>
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29 <data format="immuneml_receptors" name="html_outfile" label="ImmuneML dataset (simulated immune signals)"/>
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30 </outputs>
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31
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32
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33 <help><![CDATA[
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34
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35 This Galaxy tool can be used to implant short disease-associated motifs into an existing Repertoire dataset.
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36 Such a dataset with simulated immune signals can be used to benchmark different ML methods.
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37 Any type of repertoire dataset (experimental or simulated) can be used as a starting point for an immune event simulation, as long as it contains amino acid sequences.
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38
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39 If you instead want to simulate a synthetic dataset from scratch, start with the
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40 tool `Simulate a synthetic immune receptor or repertoire dataset <root?tool_id=immuneml_simulate_dataset>`_.
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42 For the exhaustive documentation of this tool and an example YAML specification, see the tutorial `How to simulate immune events into an existing AIRR dataset in Galaxy <https://docs.immuneml.uio.no/latest/galaxy/galaxy_simulate_signals.html>`_.
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43
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44 **Tool output**
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46 This Galaxy tool will produce the following history elements:
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48 - ImmuneML dataset (simulated immune signals): a 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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49 (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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51 - Archive: immune signal simulation: a .zip file containing the complete output folder as it was produced by immuneML. This folder
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52 contains the output of the Simulation instruction including all raw data files.
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53 Furthermore, the folder contains the complete YAML specification file for the immuneML run, the HTML output and a log file.
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56 ]]>
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57 </help>
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58
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59 </tool>