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annotate qiime2__phylogeny__raxml_rapid_bootstrap.xml @ 3:e46713e5531a draft

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author q2d2
date Thu, 25 Apr 2024 21:17:11 +0000
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children eb6c15cd603b
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 phylogeny raxml-rapid-bootstrap" id="qiime2__phylogeny__raxml_rapid_bootstrap" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Construct a phylogenetic tree with bootstrap supports using RAxML.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
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17 </requirements>
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18 <version_command>q2galaxy version phylogeny</version_command>
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19 <command detect_errors="exit_code">q2galaxy run phylogeny raxml_rapid_bootstrap '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] Aligned sequences to be used for phylogenetic reconstruction.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional] Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>
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32 <param name="rapid_bootstrap_seed" type="integer" optional="true" label="rapid_bootstrap_seed: Int" help="[optional] Specify a random seed for rapid bootstrapping. This allows you to reproduce rapid bootstrap results. If not supplied then one will be randomly chosen."/>
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33 <param name="bootstrap_replicates" type="integer" min="10" value="100" label="bootstrap_replicates: Int % Range(10, None)" help="[default: 100] The number of bootstrap searches to perform."/>
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34 <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio">
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35 <option value="Standard" selected="true">Standard</option>
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36 <option value="SSE3">SSE3</option>
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37 <option value="AVX2">AVX2</option>
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38 </param>
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39 <param name="substitution_model" type="select" label="substitution_model: Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI')" display="radio">
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40 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
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41 <option value="GTRGAMMAI">GTRGAMMAI</option>
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42 <option value="GTRCAT">GTRCAT</option>
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43 <option value="GTRCATI">GTRCATI</option>
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44 </param>
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45 </section>
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46 </inputs>
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47 <outputs>
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48 <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
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49 </outputs>
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50 <tests/>
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51 <help>
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52 QIIME 2: phylogeny raxml-rapid-bootstrap
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53 ========================================
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54 Construct a phylogenetic tree with bootstrap supports using RAxML.
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55
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56
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57 Outputs:
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58 --------
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59 :tree.qza: The resulting phylogenetic tree.
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60
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61 |
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62
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63 Description:
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64 ------------
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65 Construct a phylogenetic tree with RAxML with the addition of rapid bootstrapping support values. See: https://sco.h-its.org/exelixis/web/software/raxml/
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66
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67
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68 |
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69
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70 </help>
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71 <citations>
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72 <citation type="doi">10.1093/bioinformatics/btu033</citation>
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73 <citation type="doi">10.1080/10635150802429642</citation>
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74 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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75 </citations>
3bb5efe0ee0c planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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76 </tool>