view qiime2__quality_control__decontam_identify.xml @ 1:0036b5f124ef draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2024, QIIME 2 development team.

Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
-->
<!--
This tool was automatically generated by:
    q2galaxy (version: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<tool name="qiime2 quality-control decontam-identify" id="qiime2__quality_control__decontam_identify" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Identify contaminants</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version quality_control</version_command>
    <command detect_errors="exit_code">q2galaxy run quality_control decontam_identify '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  ASV or OTU table which contaminate sequences will be identified from">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <repeat name="metadata" min="1" help="[required]  metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter" title="metadata: Metadata">
            <conditional name="__q2galaxy__GUI__conditional__metadata__">
                <param name="type" type="select" label="metadata: Metadata">
                    <option value="tsv" selected="true">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="tsv">
                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                </when>
                <when value="qza">
                    <param name="source" type="data" format="qza" label="Metadata Source"/>
                </when>
            </conditional>
        </repeat>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="method" type="select" label="method: Str % Choices('combined', 'frequency', 'prevalence')" display="radio">
                <option value="combined">combined</option>
                <option value="frequency">frequency</option>
                <option value="prevalence" selected="true">prevalence</option>
            </param>
            <conditional name="__q2galaxy__GUI__conditional__freq_concentration_column__" label="freq_concentration_column: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="freq_concentration_column: Str" help="[optional]  Input column name that has concentration information for the samples">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="freq_concentration_column" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="freq_concentration_column" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__prev_control_column__" label="prev_control_column: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_column: Str" help="[optional]  Input column name containing experimental or control sample metadata">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="prev_control_column" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="prev_control_column" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__prev_control_indicator__" label="prev_control_indicator: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_indicator: Str" help="[optional]  indicate the control sample identifier (e.g. &quot;control&quot; or &quot;blank&quot;)">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="prev_control_indicator" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="prev_control_indicator" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="decontam_scores" format="qza" label="${tool.name} on ${on_string}: decontam_scores.qza" from_work_dir="decontam_scores.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: quality-control decontam-identify
==========================================
Identify contaminants


Outputs:
--------
:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each ASV or OTU on how likely they are to be a contaminant sequence

|  

Description:
------------
This method identifies contaminant sequences from an OTU or ASV table and reports them to the user


|  

</help>
    <citations>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>