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annotate qiime2__quality_control__bowtie2_build.xml @ 1:dc6b98098f4f draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:59:28 +0000
parents 78420e8bfd49
children ea81dc3914f8
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, 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: 2022.11.1)
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10 for:
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11 qiime2 (version: 2022.11.1)
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12 -->
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13 <tool name="qiime2 quality-control bowtie2-build" id="qiime2__quality_control__bowtie2_build" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Build bowtie2 index from reference sequences.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.11</container>
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17 </requirements>
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18 <version_command>q2galaxy version quality_control</version_command>
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19 <command detect_errors="exit_code">q2galaxy run quality_control bowtie2_build '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Reference sequences used to build bowtie2 index.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Sequence]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1] Number of threads to launch"/>
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32 </section>
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33 </inputs>
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34 <outputs>
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35 <data name="database" format="qza" label="${tool.name} on ${on_string}: database.qza" from_work_dir="database.qza"/>
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36 </outputs>
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37 <tests/>
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38 <help>
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39 QIIME 2: quality-control bowtie2-build
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40 ======================================
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41 Build bowtie2 index from reference sequences.
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42
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43
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44 Outputs:
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45 --------
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46 :database.qza: Bowtie2 index.
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47
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48 |
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49
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50 Description:
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51 ------------
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52 Build bowtie2 index from reference sequences.
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53
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54
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55 |
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56
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57 </help>
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58 <citations>
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59 <citation type="bibtex">@article{cite1,
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60 author = {Langmead, Ben and Salzberg, Steven L},
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61 journal = {Nature methods},
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62 number = {4},
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63 pages = {357},
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64 publisher = {Nature Publishing Group},
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65 title = {Fast gapped-read alignment with Bowtie 2},
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66 volume = {9},
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67 year = {2012}
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68 }
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69 </citation>
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70 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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71 </citations>
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72 </tool>