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author q2d2
date Thu, 08 Jun 2023 19:51:15 +0000
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2e8e3258af39 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
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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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4
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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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Removes contaminant</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</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="paths"/>
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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] Output table from decontam identify">
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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] ASV or OTU table which contaminate sequences will be identified from">
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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 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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37 <param name="threshold" type="float" value="0.1" label="threshold: Float" help="[default: 0.1] Select threshold cutoff for decontam algorithm scores"/>
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38 </section>
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39 </inputs>
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40 <outputs>
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41 <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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42 </outputs>
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43 <tests/>
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44 <help>
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45 QIIME 2: quality-control decontam-remove
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46 ========================================
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47 Removes contaminant
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48
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49
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50 Outputs:
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51 --------
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52 :filtered_table.qza: The resulting feature table of scores once contaminants are removed
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53
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54 |
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55
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56 Description:
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57 ------------
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58 This method removes contaminant sequences from an OTU or ASV table and returns the amended table to the user
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59
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60
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61 |
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62
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63 </help>
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64 <citations>
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65 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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66 </citations>
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67 </tool>