Mercurial > repos > q2d2 > qiime2__quality_control__decontam_remove

annotate qiime2__quality_control__decontam_remove.xml @ 2:ceb8db9c0509 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:30:21 +0000
parents 9edda646c9dd
children 239447c3062a
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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 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Remove contaminants</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 quality_control</version_command>
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19 <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$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="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required] Pre-feature decontam scores.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[DecontamScore]"/>
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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[DecontamScore]']</validator>
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29 </param>
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30 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table from which contaminants will be removed.">
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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="FeatureTable[Frequency]"/>
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33 </options>
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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35 </param>
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36 <param name="rep_seqs" type="data" format="qza" label="rep_seqs: FeatureData[Sequence]" help="[required] Feature representative sequences from which contaminants will be removed.">
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37 <options options_filter_attribute="metadata.semantic_type">
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38 <filter type="add_value" value="FeatureData[Sequence]"/>
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39 </options>
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40 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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41 </param>
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42 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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43 <param name="threshold" type="float" min="0.0" max="1.0" value="0.1" label="threshold: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.1] Decontam score threshold. Features with a score less than or equal to this threshold will be removed."/>
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
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48 <data name="filtered_rep_seqs" format="qza" label="${tool.name} on ${on_string}: filtered_rep_seqs.qza" from_work_dir="filtered_rep_seqs.qza"/>
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49 </outputs>
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50 <tests/>
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51 <help>
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52 QIIME 2: quality-control decontam-remove
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53 ========================================
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54 Remove contaminants
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55
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56
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57 Outputs:
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58 --------
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59 :filtered_table.qza: Feature table with contaminants removed.
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60 :filtered_rep_seqs.qza: Feature representative sequences with contaminants removed.
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61
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62 |
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64 Description:
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65 ------------
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66 Remove contaminant sequences from a feature table and the associated representative sequences.
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67
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69 |
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71 </help>
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72 <citations>
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73 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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74 </citations>
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75 </tool>