Mercurial > repos > q2d2 > qiime2__deblur__visualize_stats

annotate qiime2__deblur__visualize_stats.xml @ 4:e02092a0b2db draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:17:47 +0000
parents d1b15724ff2b
children 2e4eafd6f1f6
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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: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 deblur visualize-stats" id="qiime2__deblur__visualize_stats" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Visualize Deblur stats per sample.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version deblur</version_command>
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19 <command detect_errors="exit_code">q2galaxy run deblur visualize_stats '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="deblur_stats" type="data" format="qza" label="deblur_stats: DeblurStats" help="[required] Summary statistics of the Deblur process.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="DeblurStats"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DeblurStats']</validator>
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="deblur_stats" value="visualize_stats.test0.deblur-stats.qza" ftype="qza"/>
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37 <output name="visualization" ftype="qzv">
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38 <assert_contents>
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39 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
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40 <has_line_matching expression="type: Visualization"/>
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41 </has_archive_member>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help>
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47 QIIME 2: deblur visualize-stats
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48 ===============================
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49 Visualize Deblur stats per sample.
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50
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51
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52 Outputs:
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53 --------
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54 :visualization.qzv: &lt;no description&gt;
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55
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56 |
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57
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58 Description:
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59 ------------
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60 Display Deblur statistics per sample
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61
1
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62 Examples:
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63 ---------
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64
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65 visualize_stats
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66 ***************
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67 Using the ``qiime2 deblur visualize-stats`` tool:
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68 #. Set *"deblur_stats"* to ``#: deblur-stats.qza``
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69 #. Press the ``Execute`` button.
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70
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71 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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72 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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73
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74 .. list-table::
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75 :align: left
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76 :header-rows: 1
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77
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78 * - History Name
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79 - *"Name"* to set (be sure to press ``Save``)
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80 * - ``#: qiime2 deblur visualize-stats [...] : visualization.qzv``
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81 - ``deblur-stats-viz.qzv``
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82
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83
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84 |
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85
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86 </help>
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87 <citations>
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88 <citation type="bibtex">@article{cite1,
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89 author = {Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob},
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90 journal = {MSystems},
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91 number = {2},
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92 pages = {e00191--16},
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93 publisher = {Am Soc Microbiol},
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94 title = {Deblur rapidly resolves single-nucleotide community sequence patterns},
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95 volume = {2},
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96 year = {2017}
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97 }
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98 </citation>
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99 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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100 </citations>
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101 </tool>