comparison qiime2__cutadapt__trim_single.xml @ 6:b652bc0bd0ff draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit b1fccfb38b4873cd4699743033449014a2978e7d

5:f8d5e0d4dfec

<?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 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Find and remove adapters in demultiplexed single-end sequences.</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 cutadapt</version_command>
    <command detect_errors="exit_code">q2galaxy run cutadapt trim_single '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>

                        <valid initial="string.printable"/>
                    </sanitizer>
                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
                </param>
            </repeat>
            <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1]  Maximum allowed error rate."/>
            <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="indels: Bool" help="[default: Yes]  Allow insertions or deletions of bases when matching adapters."/>
            <param name="times" type="integer" min="1" value="1" label="times: Int % Range(1, None)" help="[default: 1]  Remove multiple occurrences of an adapter if it is repeated, up to `times` times."/>
            <param name="overlap" type="integer" min="1" value="3" label="overlap: Int % Range(1, None)" help="[default: 3]  Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."/>
            <param name="match_read_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="match_read_wildcards: Bool" help="[default: No]  Interpret IUPAC wildcards (e.g., N) in reads."/>

6:b652bc0bd0ff

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.4.0)
for:
    qiime2 (version: 2025.4.0)
-->
<tool name="qiime2 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Find and remove adapters in demultiplexed single-end sequences.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
    </requirements>
    <version_command>q2galaxy version cutadapt</version_command>
    <command detect_errors="exit_code">q2galaxy run cutadapt trim_single '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>

                        <valid initial="string.printable"/>
                    </sanitizer>
                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
                </param>
            </repeat>
            <param name="cut" type="integer" value="0" label="cut: Int" help="[default: 0]  Unconditionally remove bases from the beginning or end of each read. Cutting is applied before adapter trimming. Use a positive integer to remove bases from the 5' end and a negative integer to remove bases from the 3' end."/>
            <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1]  Maximum allowed error rate."/>
            <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="indels: Bool" help="[default: Yes]  Allow insertions or deletions of bases when matching adapters."/>
            <param name="times" type="integer" min="1" value="1" label="times: Int % Range(1, None)" help="[default: 1]  Remove multiple occurrences of an adapter if it is repeated, up to `times` times."/>
            <param name="overlap" type="integer" min="1" value="3" label="overlap: Int % Range(1, None)" help="[default: 3]  Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."/>
            <param name="match_read_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="match_read_wildcards: Bool" help="[default: No]  Interpret IUPAC wildcards (e.g., N) in reads."/>