comparison qiime2__vsearch__uchime_ref.xml @ 3:e9b3abbe198e draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

2:7dbbd990440e

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2023.5.0)
for:
    qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 vsearch uchime-ref" id="qiime2__vsearch__uchime_ref" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Reference-based chimera filtering with vsearch.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version vsearch</version_command>
    <command detect_errors="exit_code">q2galaxy run vsearch uchime_ref '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The feature sequences to be chimera-checked.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>

            <param name="dn" type="float" min="0.0" value="1.4" label="dn: Float % Range(0.0, None)" help="[default: 1.4]  No vote pseudo-count, corresponding to the parameter n in the chimera scoring function."/>
            <param name="mindiffs" type="integer" min="1" value="3" label="mindiffs: Int % Range(1, None)" help="[default: 3]  Minimum number of differences per segment."/>
            <param name="mindiv" type="float" min="0.0" value="0.8" label="mindiv: Float % Range(0.0, None)" help="[default: 0.8]  Minimum divergence from closest parent."/>
            <param name="minh" type="float" min="0.0" max="1.0" value="0.28" label="minh: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.28]  Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity."/>
            <param name="xn" type="float" min="1.000001" value="8.0" label="xn: Float % Range(1.0, None, inclusive_start=False)" help="[default: 8.0]  No vote weight, corresponding to the parameter beta in the scoring function."/>
            <param name="threads" type="integer" min="0" max="256" value="1" label="threads: Int % Range(0, 256, inclusive_end=True)" help="[default: 1]  The number of threads to use for computation. Passing 0 will launch one thread per CPU core."/>
        </section>
    </inputs>
    <outputs>
        <data name="chimeras" format="qza" label="${tool.name} on ${on_string}: chimeras.qza" from_work_dir="chimeras.qza"/>
        <data name="nonchimeras" format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" from_work_dir="nonchimeras.qza"/>

3:e9b3abbe198e

<?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 vsearch uchime-ref" id="qiime2__vsearch__uchime_ref" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Reference-based chimera filtering with vsearch.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version vsearch</version_command>
    <command detect_errors="exit_code">q2galaxy run vsearch uchime_ref '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The feature sequences to be chimera-checked.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>

            <param name="dn" type="float" min="0.0" value="1.4" label="dn: Float % Range(0.0, None)" help="[default: 1.4]  No vote pseudo-count, corresponding to the parameter n in the chimera scoring function."/>
            <param name="mindiffs" type="integer" min="1" value="3" label="mindiffs: Int % Range(1, None)" help="[default: 3]  Minimum number of differences per segment."/>
            <param name="mindiv" type="float" min="0.0" value="0.8" label="mindiv: Float % Range(0.0, None)" help="[default: 0.8]  Minimum divergence from closest parent."/>
            <param name="minh" type="float" min="0.0" max="1.0" value="0.28" label="minh: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.28]  Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity."/>
            <param name="xn" type="float" min="1.000001" value="8.0" label="xn: Float % Range(1.0, None, inclusive_start=False)" help="[default: 8.0]  No vote weight, corresponding to the parameter beta in the scoring function."/>
        </section>
    </inputs>
    <outputs>
        <data name="chimeras" format="qza" label="${tool.name} on ${on_string}: chimeras.qza" from_work_dir="chimeras.qza"/>
        <data name="nonchimeras" format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" from_work_dir="nonchimeras.qza"/>