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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 20:00:02 +0000
parents 6acd7854064f
children
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68c96beb62cf planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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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b770f74843a4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 vsearch fastq-stats" id="qiime2__vsearch__fastq_stats" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Fastq stats with vsearch.</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 vsearch</version_command>
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22 <command detect_errors="exit_code">q2galaxy run vsearch fastq_stats '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="sequences" type="data" format="qza" label="sequences: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required] Fastq sequences">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
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30 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
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31 </options>
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32 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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37 </outputs>
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38 <tests/>
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39 <help>
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40 QIIME 2: vsearch fastq-stats
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41 ============================
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42 Fastq stats with vsearch.
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43
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44
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45 Outputs:
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46 --------
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47 :visualization.qzv: &lt;no description&gt;
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48
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49 |
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50
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51 Description:
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52 ------------
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53 A fastq overview via vsearch's fastq_stats, fastq_eestats and fastq_eestats2 utilities. Please see https://github.com/torognes/vsearch for detailed documentation of these tools.
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54
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55
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56 |
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57
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58 </help>
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59 <citations>
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60 <citation type="doi">10.7717/peerj.2584</citation>
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61 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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62 </citations>
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63 </tool>