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author q2d2
date Wed, 30 Oct 2024 19:54:20 +0000
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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: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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13 <tool name="qiime2 quality-control evaluate-seqs" id="qiime2__quality_control__evaluate_seqs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Compare query (observed) vs. reference (expected) sequences.</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 quality_control</version_command>
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22 <command detect_errors="exit_code">q2galaxy run quality_control evaluate_seqs '$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="query_sequences" type="data" format="qza" label="query_sequences: FeatureData[Sequence]" help="[required] Sequences to test for exclusion">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[Sequence]"/>
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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 ['FeatureData[Sequence]']</validator>
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32 </param>
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33 <param name="reference_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required] Reference sequences to align against feature sequences">
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34 <options options_filter_attribute="metadata.semantic_type">
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35 <filter type="add_value" value="FeatureData[Sequence]"/>
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36 </options>
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37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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38 </param>
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39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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40 <param name="show_alignments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="show_alignments: Bool" help="[default: No] Option to plot pairwise alignments of query sequences and their top hits."/>
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41 </section>
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42 </inputs>
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43 <outputs>
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44 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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45 </outputs>
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46 <tests/>
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47 <help>
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48 QIIME 2: quality-control evaluate-seqs
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49 ======================================
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50 Compare query (observed) vs. reference (expected) sequences.
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51
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52
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53 Outputs:
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54 --------
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55 :visualization.qzv: &lt;no description&gt;
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56
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57 |
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58
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59 Description:
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60 ------------
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61 This action aligns a set of query (e.g., observed) sequences against a set of reference (e.g., expected) sequences to evaluate the quality of alignment. The intended use is to align observed sequences against expected sequences (e.g., from a mock community) to determine the frequency of mismatches between observed sequences and the most similar expected sequences, e.g., as a measure of sequencing/method error. However, any sequences may be provided as input to generate a report on pairwise alignment quality against a set of reference sequences.
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62
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63
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64 |
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65
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66 </help>
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67 <citations>
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68 <citation type="doi">10.1186/1471-2105-10-421</citation>
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69 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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70 </citations>
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71 </tool>