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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:35:59 +0000
parents c4a4ba3c7a9c
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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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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 alignment mafft" id="qiime2__alignment__mafft" version="2024.10.0+q2galaxy.2024.10.0" 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 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version alignment</version_command>
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22 <command detect_errors="exit_code">q2galaxy run alignment mafft '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] The sequences to be aligned.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[Sequence]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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32 </param>
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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34 <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No] This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default"/>
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35 </section>
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36 </inputs>
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37 <outputs>
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38 <data name="alignment" format="qza" label="${tool.name} on ${on_string}: alignment.qza" from_work_dir="alignment.qza"/>
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39 </outputs>
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40 <tests/>
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41 <help>
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42 QIIME 2: alignment mafft
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43 ========================
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44 De novo multiple sequence alignment with MAFFT
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45
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46
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47 Outputs:
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48 --------
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49 :alignment.qza: The aligned sequences.
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50
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51 |
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52
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53 Description:
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54 ------------
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55 Perform de novo multiple sequence alignment using MAFFT.
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56
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57
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58 |
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59
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60 </help>
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61 <citations>
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62 <citation type="doi">10.1093/molbev/mst010</citation>
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63 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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64 </citations>
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65 </tool>