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author q2d2
date Wed, 30 Oct 2024 19:35:56 +0000
parents 51e7e9d2c302
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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-add" id="qiime2__alignment__mafft_add" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Add sequences to 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_add '$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="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] The alignment to which sequences should be added.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
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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[AlignedSequence]']</validator>
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32 </param>
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33 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] The sequences to be added.">
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34 <options options_filter_attribute="metadata.semantic_type">
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35 <filter type="add_value" value="FeatureData[Sequence]"/>
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36 </options>
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37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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38 </param>
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39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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40 <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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41 <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No] Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
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42 <param name="keeplength" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="keeplength: Bool" help="[default: No] If selected, the alignment length will be unchanged. Any added sequence that would otherwise introduce new insertions into the alignment, will have those insertions deleted, to preserve original alignment length."/>
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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="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.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: alignment mafft-add
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51 ============================
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52 Add sequences to multiple sequence alignment with MAFFT.
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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 :expanded_alignment.qza: Alignment containing the provided aligned and unaligned sequences.
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58
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59 |
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61 Description:
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62 ------------
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63 Add new sequences to an existing alignment with MAFFT.
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64
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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">10.1093/molbev/mst010</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>