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annotate qiime2__quality_control__exclude_seqs.xml @ 2:cf4229cd0a05 draft

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author q2d2
date Thu, 08 Jun 2023 19:50:53 +0000
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children 9d29d1b06e2c
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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: 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 exclude-seqs" id="qiime2__quality_control__exclude_seqs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Exclude sequences by alignment</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 exclude_seqs '$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="query_sequences" type="data" format="qza" label="query_sequences: FeatureData[Sequence]" help="[required] Sequences to test for exclusion">
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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 <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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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="FeatureData[Sequence]"/>
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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 ['FeatureData[Sequence]']</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="method" type="select" label="method: Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')²" help="[default: 'blast'] Alignment method to use for matching feature sequences against reference sequences">
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38 <option value="blast" selected="true">blast (Str)</option>
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39 <option value="blastn-short">blastn-short (Str)</option>
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40 <option value="vsearch">vsearch (Str)</option>
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41 </param>
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42 <param name="perc_identity" type="float" min="0.0" max="1.0" value="0.97" label="perc_identity: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.97] Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]"/>
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43 <param name="evalue" type="float" optional="true" label="evalue: Float" help="[optional] BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default."/>
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44 <param name="perc_query_aligned" type="float" value="0.97" label="perc_query_aligned: Float" help="[default: 0.97] Percent of query sequence that must align to reference in order to be accepted as a hit."/>
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45 <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] Number of jobs to execute. Only applies to vsearch method."/>
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46 <param name="left_justify" type="select" label="left_justify: Bool % Choices(False)¹ | Bool²" help="[default: No] Reject match if the pairwise alignment begins with gaps">
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47 <option value="__q2galaxy__::literal::False" selected="true">No (Bool)</option>
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48 <option value="__q2galaxy__::literal::True">Yes (Bool)</option>
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49 </param>
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50 </section>
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51 </inputs>
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52 <outputs>
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53 <data name="sequence_hits" format="qza" label="${tool.name} on ${on_string}: sequence_hits.qza" from_work_dir="sequence_hits.qza"/>
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54 <data name="sequence_misses" format="qza" label="${tool.name} on ${on_string}: sequence_misses.qza" from_work_dir="sequence_misses.qza"/>
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55 </outputs>
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56 <tests/>
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57 <help>
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58 QIIME 2: quality-control exclude-seqs
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59 =====================================
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60 Exclude sequences by alignment
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61
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63 Outputs:
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64 --------
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65 :sequence_hits.qza: Subset of feature sequences that align to reference sequences
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66 :sequence_misses.qza: Subset of feature sequences that do not align to reference sequences
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67
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68 |
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70 Description:
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71 ------------
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72 This method aligns feature sequences to a set of reference sequences to identify sequences that hit/miss the reference within a specified perc_identity, evalue, and perc_query_aligned. This method could be used to define a positive filter, e.g., extract only feature sequences that align to a certain clade of bacteria; or to define a negative filter, e.g., identify sequences that align to contaminant or human DNA sequences that should be excluded from subsequent analyses. Note that filtering is performed based on the perc_identity, perc_query_aligned, and evalue thresholds (the latter only if method==BLAST and an evalue is set). Set perc_identity==0 and/or perc_query_aligned==0 to disable these filtering thresholds as necessary.
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75 |
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77 </help>
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78 <citations>
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79 <citation type="doi">10.1186/1471-2105-10-421</citation>
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80 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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81 </citations>
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82 </tool>