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comparison 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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1:9edda646c9dd 2:ceb8db9c0509
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2024.2.1) 9 q2galaxy (version: 2024.5.0)
10 for: 10 for:
11 qiime2 (version: 2024.2.0) 11 qiime2 (version: 2024.5.0)
12 --> 12 -->
13 <tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> 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">
14 <description>Removes contaminant</description> 14 <description>Remove contaminants</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version quality_control</version_command> 18 <version_command>q2galaxy version quality_control</version_command>
19 <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required] Output table from decontam identify"> 24 <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required] Pre-feature decontam scores.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="FeatureData[DecontamScore]"/> 26 <filter type="add_value" value="FeatureData[DecontamScore]"/>
27 </options> 27 </options>
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]']</validator> 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]']</validator>
29 </param> 29 </param>
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"> 30 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table from which contaminants will be removed.">
31 <options options_filter_attribute="metadata.semantic_type"> 31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="FeatureTable[Frequency]"/> 32 <filter type="add_value" value="FeatureTable[Frequency]"/>
33 </options> 33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> 34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
35 </param> 35 </param>
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.">
37 <options options_filter_attribute="metadata.semantic_type">
38 <filter type="add_value" value="FeatureData[Sequence]"/>
39 </options>
40 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
41 </param>
36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 42 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
37 <param name="threshold" type="float" value="0.1" label="threshold: Float" help="[default: 0.1] Select threshold cutoff for decontam algorithm scores"/> 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."/>
38 </section> 44 </section>
39 </inputs> 45 </inputs>
40 <outputs> 46 <outputs>
41 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> 47 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
48 <data name="filtered_rep_seqs" format="qza" label="${tool.name} on ${on_string}: filtered_rep_seqs.qza" from_work_dir="filtered_rep_seqs.qza"/>
42 </outputs> 49 </outputs>
43 <tests/> 50 <tests/>
44 <help> 51 <help>
45 QIIME 2: quality-control decontam-remove 52 QIIME 2: quality-control decontam-remove
46 ======================================== 53 ========================================
47 Removes contaminant 54 Remove contaminants
48 55
49 56
50 Outputs: 57 Outputs:
51 -------- 58 --------
52 :filtered_table.qza: The resulting feature table of scores once contaminants are removed 59 :filtered_table.qza: Feature table with contaminants removed.
60 :filtered_rep_seqs.qza: Feature representative sequences with contaminants removed.
53 61
54 | 62 |
55 63
56 Description: 64 Description:
57 ------------ 65 ------------
58 This method removes contaminant sequences from an OTU or ASV table and returns the amended table to the user 66 Remove contaminant sequences from a feature table and the associated representative sequences.
59 67
60 68
61 | 69 |
62 70
63 </help> 71 </help>