Mercurial > repos > q2d2 > qiime2__rescript__evaluate_seqs
annotate qiime2__rescript__evaluate_seqs.xml @ 1:6ac548ed17c3 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:31:06 +0000 |
parents | 54d62a2792e8 |
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54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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1 <?xml version='1.0' encoding='utf-8'?> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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2 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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3 Copyright (c) 2024, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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4 |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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6 --> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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8 This tool was automatically generated by: |
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6ac548ed17c3
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit c7e80dcda727ce63b42aa8a946e9330310929797
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9 q2galaxy (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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10 for: |
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6ac548ed17c3
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit c7e80dcda727ce63b42aa8a946e9330310929797
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11 qiime2 (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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12 --> |
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6ac548ed17c3
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit c7e80dcda727ce63b42aa8a946e9330310929797
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13 <tool name="qiime2 rescript evaluate-seqs" id="qiime2__rescript__evaluate_seqs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> |
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54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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14 <description>Compute summary statistics on sequence artifact(s).</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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15 <requirements> |
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6ac548ed17c3
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit c7e80dcda727ce63b42aa8a946e9330310929797
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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17 </requirements> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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18 <version_command>q2galaxy version rescript</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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19 <command detect_errors="exit_code">q2galaxy run rescript evaluate_seqs '$inputs'</command> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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20 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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22 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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24 <param name="sequences" type="data" format="qza" label="sequences: List[FeatureData[Sequence]]" help="[required] One or more sets of sequences to evaluate." multiple="true"> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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25 <options options_filter_attribute="metadata.semantic_type"> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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26 <filter type="add_value" value="FeatureData[Sequence]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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27 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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28 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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29 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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30 <repeat name="labels" help="[optional] List of labels to use for labeling evaluation results in the resulting visualization. Inputs are labeled with labels in the order that each is input. If there are fewer labels than inputs (or no labels), unnamed inputs are labeled numerically in sequential order. Extra labels are ignored." title="labels: List[Str]"> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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31 <param name="element" type="text" label="element: Str" help="[required]"> |
54d62a2792e8
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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32 <sanitizer> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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33 <valid initial="string.printable"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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34 </sanitizer> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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35 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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36 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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37 </repeat> |
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38 <repeat name="kmer_lengths" help="[optional] Sequence kmer lengths to optionally use for entropy calculation. Warning: kmer entropy calculations may be time-consuming for large sequence sets." title="kmer_lengths: List[Int % Range(1, None)]"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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39 <param name="element" type="integer" min="1" value="" label="element: Int % Range(1, None)" help="[required]"/> |
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40 </repeat> |
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41 <param name="subsample_kmers" type="float" min="1e-06" max="1" value="1.0" label="subsample_kmers: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 1.0] Optionally subsample sequences prior to kmer entropy measurement. A fraction of the input sequences will be randomly subsampled at the specified value."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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42 <param name="palette" type="select" label="palette: Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'cividis', 'terrain', 'rainbow', 'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', 'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic')"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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43 <option value="Set1">Set1</option> |
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44 <option value="Set2">Set2</option> |
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45 <option value="Set3">Set3</option> |
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46 <option value="Pastel1">Pastel1</option> |
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47 <option value="Pastel2">Pastel2</option> |
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48 <option value="Paired">Paired</option> |
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49 <option value="Accent">Accent</option> |
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50 <option value="Dark2">Dark2</option> |
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51 <option value="tab10">tab10</option> |
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52 <option value="tab20">tab20</option> |
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53 <option value="tab20b">tab20b</option> |
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54 <option value="tab20c">tab20c</option> |
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55 <option value="viridis" selected="true">viridis</option> |
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56 <option value="plasma">plasma</option> |
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57 <option value="inferno">inferno</option> |
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58 <option value="magma">magma</option> |
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59 <option value="cividis">cividis</option> |
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60 <option value="terrain">terrain</option> |
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61 <option value="rainbow">rainbow</option> |
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62 <option value="PiYG">PiYG</option> |
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63 <option value="PRGn">PRGn</option> |
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64 <option value="BrBG">BrBG</option> |
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65 <option value="PuOr">PuOr</option> |
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66 <option value="RdGy">RdGy</option> |
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67 <option value="RdBu">RdBu</option> |
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68 <option value="RdYlBu">RdYlBu</option> |
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69 <option value="RdYlGn">RdYlGn</option> |
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70 <option value="Spectral">Spectral</option> |
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71 <option value="coolwarm">coolwarm</option> |
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72 <option value="bwr">bwr</option> |
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73 <option value="seismic">seismic</option> |
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74 </param> |
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75 </section> |
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76 </inputs> |
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77 <outputs> |
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78 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> |
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79 </outputs> |
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80 <tests/> |
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81 <help> |
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82 QIIME 2: rescript evaluate-seqs |
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83 =============================== |
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84 Compute summary statistics on sequence artifact(s). |
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85 |
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86 |
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87 Outputs: |
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88 -------- |
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89 :visualization.qzv: <no description> |
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90 |
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91 | |
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92 |
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93 Description: |
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94 ------------ |
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95 Compute summary statistics on sequence artifact(s) and visualize. Summary statistics include the number of unique sequences, sequence entropy, kmer entropy, and sequence length distributions. This action is useful for both reference taxonomies and classification results. |
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96 |
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97 |
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98 | |
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99 |
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100 </help> |
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101 <citations> |
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102 <citation type="doi">10.1371/journal.pcbi.1009581</citation> |
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103 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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104 </citations> |
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105 </tool> |