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annotate qiime2__phylogeny__fasttree.xml @ 1:54e234742860 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:58:25 +0000
parents c9eafd561cc4
children 977e2ec8beb0
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, 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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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2022.11.1)
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10 for:
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11 qiime2 (version: 2022.11.1)
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12 -->
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13 <tool name="qiime2 phylogeny fasttree" id="qiime2__phylogeny__fasttree" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Construct a phylogenetic tree with FastTree.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.11</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 fasttree '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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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 <conditional name="__q2galaxy__GUI__conditional__n_threads__">
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32 <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of threads. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores)">
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33 <option value="auto">auto (Str)</option>
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34 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
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35 </param>
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36 <when value="auto">
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37 <param name="n_threads" type="hidden" value="auto"/>
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38 </when>
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39 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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40 <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1] The number of threads. Using more than one thread runs the non-deterministic variant of `FastTree` (`FastTreeMP`), and may result in a different tree than single-threading. See http://www.microbesonline.org/fasttree/#OpenMP for details. (Use `auto` to automatically use all available cores)"/>
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41 </when>
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42 </conditional>
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43 </section>
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44 </inputs>
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45 <outputs>
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46 <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
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47 </outputs>
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48 <tests/>
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49 <help>
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50 QIIME 2: phylogeny fasttree
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51 ===========================
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52 Construct a phylogenetic tree with FastTree.
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53
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54
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55 Outputs:
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56 --------
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57 :tree.qza: The resulting phylogenetic tree.
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58
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59 |
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60
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61 Description:
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62 ------------
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63 Construct a phylogenetic tree with FastTree.
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64
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65
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66 |
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67
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68 </help>
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69 <citations>
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70 <citation type="doi">10.1371/journal.pone.0009490</citation>
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71 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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72 </citations>
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73 </tool>