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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:35:53 +0000
parents 1d37aa0aed4f
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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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12 -->
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13 <tool name="qiime2 alignment mask" id="qiime2__alignment__mask" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Positional conservation and gap filtering.</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 alignment</version_command>
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22 <command detect_errors="exit_code">q2galaxy run alignment mask '$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="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] The alignment to be masked.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
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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[AlignedSequence]']</validator>
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32 </param>
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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34 <param name="max_gap_frequency" type="float" min="0" max="1" value="1.0" label="max_gap_frequency: Float % Range(0, 1, inclusive_end=True)" help="[default: 1.0] The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency."/>
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35 <param name="min_conservation" type="float" min="0" max="1" value="0.4" label="min_conservation: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.4] The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences."/>
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36 </section>
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37 </inputs>
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38 <outputs>
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39 <data name="masked_alignment" format="qza" label="${tool.name} on ${on_string}: masked_alignment.qza" from_work_dir="masked_alignment.qza"/>
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40 </outputs>
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41 <tests/>
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42 <help>
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43 QIIME 2: alignment mask
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44 =======================
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45 Positional conservation and gap filtering.
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46
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47
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48 Outputs:
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49 --------
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50 :masked_alignment.qza: The masked alignment.
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51
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52 |
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53
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54 Description:
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55 ------------
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56 Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
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57
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58
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59 |
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60
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61 </help>
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62 <citations>
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63 <citation type="bibtex">@incollection{cite1,
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64 address = {New York},
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65 author = {Lane, DJ},
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66 booktitle = {Nucleic Acid Techniques in Bacterial Systematics},
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67 editor = {Stackebrandt, E and Goodfellow, M},
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68 pages = {115--175},
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69 publisher = {John Wiley and Sons},
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70 title = {16S/23S rRNA sequencing},
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71 year = {1991}
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72 }
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73 </citation>
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74 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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75 </citations>
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76 </tool>