view qiime2__quality_control__decontam_remove.xml @ 3:239447c3062a draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 5f71b597c9495eae67a447744fded834f56ca1f7

<?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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Remove contaminants</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version quality_control</version_command>
    <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required]  Pre-feature decontam scores.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[DecontamScore]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]']</validator>
        </param>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table from which contaminants will be removed.">
            <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>
        <param name="rep_seqs" type="data" format="qza" label="rep_seqs: FeatureData[Sequence]" help="[required]  Feature representative sequences from which contaminants will be removed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <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."/>
        </section>
    </inputs>
    <outputs>
        <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
        <data name="filtered_rep_seqs" format="qza" label="${tool.name} on ${on_string}: filtered_rep_seqs.qza" from_work_dir="filtered_rep_seqs.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: quality-control decontam-remove
========================================
Remove contaminants


Outputs:
--------
:filtered_table.qza: Feature table with contaminants removed.
:filtered_rep_seqs.qza: Feature representative sequences with contaminants removed.

|  

Description:
------------
Remove contaminant sequences from a feature table and the associated representative sequences.


|  

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