Mercurial > repos > q2d2 > qiime2__deblur__visualize_stats

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:37:07 +0000
parents e02092a0b2db
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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:
5
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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 deblur visualize-stats" id="qiime2__deblur__visualize_stats" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Visualize Deblur stats per sample.</description>
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15 <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 deblur</version_command>
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22 <command detect_errors="exit_code">q2galaxy run deblur visualize_stats '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="deblur_stats" type="data" format="qza" label="deblur_stats: DeblurStats" help="[required] Summary statistics of the Deblur process.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="DeblurStats"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DeblurStats']</validator>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="deblur_stats" value="visualize_stats.test0.deblur-stats.qza" ftype="qza"/>
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40 <output name="visualization" ftype="qzv">
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41 <assert_contents>
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42 <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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43 <has_line_matching expression="type: Visualization"/>
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44 </has_archive_member>
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49 <help>
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50 QIIME 2: deblur visualize-stats
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51 ===============================
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52 Visualize Deblur stats per sample.
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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 :visualization.qzv: &lt;no description&gt;
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58
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59 |
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60
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61 Description:
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62 ------------
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63 Display Deblur statistics per sample
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64
1
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65 Examples:
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66 ---------
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67
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68 visualize_stats
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69 ***************
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70 Using the ``qiime2 deblur visualize-stats`` tool:
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71 #. Set *"deblur_stats"* to ``#: deblur-stats.qza``
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72 #. Press the ``Execute`` button.
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73
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74 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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75 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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76
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77 .. list-table::
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78 :align: left
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79 :header-rows: 1
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81 * - History Name
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82 - *"Name"* to set (be sure to press ``Save``)
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83 * - ``#: qiime2 deblur visualize-stats [...] : visualization.qzv``
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84 - ``deblur-stats-viz.qzv``
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85
0
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86
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87 |
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88
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89 </help>
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90 <citations>
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91 <citation type="bibtex">@article{cite1,
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92 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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93 journal = {MSystems},
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94 number = {2},
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95 pages = {e00191--16},
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96 publisher = {Am Soc Microbiol},
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97 title = {Deblur rapidly resolves single-nucleotide community sequence patterns},
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98 volume = {2},
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99 year = {2017}
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100 }
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101 </citation>
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102 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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103 </citations>
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104 </tool>