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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:04:20 +0000
parents f393282d35ee
children a0a48c15c573
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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 alignment mafft" id="qiime2__alignment__mafft" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>De novo multiple sequence alignment with MAFFT</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 alignment</version_command>
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19 <command detect_errors="exit_code">q2galaxy run alignment mafft '$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="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] The sequences to be aligned.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Sequence]"/>
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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[Sequence]']</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. (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. (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 <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No] This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data name="alignment" format="qza" label="${tool.name} on ${on_string}: alignment.qza" from_work_dir="alignment.qza"/>
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48 </outputs>
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49 <tests/>
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50 <help>
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51 QIIME 2: alignment mafft
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52 ========================
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53 De novo multiple sequence alignment with MAFFT
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54
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55
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56 Outputs:
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57 --------
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58 :alignment.qza: The aligned sequences.
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59
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60 |
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61
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62 Description:
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63 ------------
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64 Perform de novo multiple sequence alignment using MAFFT.
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65
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66
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67 |
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68
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69 </help>
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70 <citations>
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71 <citation type="doi">10.1093/molbev/mst010</citation>
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72 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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73 </citations>
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74 </tool>