comparison qiime2__cutadapt__trim_paired.xml @ 3:d3cdc3eafc41 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

2:b7fc07bacdb2

<?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 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version cutadapt</version_command>
    <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[PairedEndSequencesWithQuality]" help="[required]  The paired-end sequences to be trimmed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1]  Number of CPU cores to use."/>
            <repeat name="adapter_f" help="[optional]  Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is &quot;framed&quot; by a 5' and a 3' adapter, use this parameter to define a &quot;linked&quot; primer - see https://cutadapt.readthedocs.io for complete details." title="adapter_f: List[Str]">
                <param name="element" type="text" label="element: Str" help="[required]">
                    <sanitizer>
                        <valid initial="string.printable"/>
                    </sanitizer>

3:d3cdc3eafc41

<?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 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version cutadapt</version_command>
    <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[PairedEndSequencesWithQuality]" help="[required]  The paired-end sequences to be trimmed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <repeat name="adapter_f" help="[optional]  Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is &quot;framed&quot; by a 5' and a 3' adapter, use this parameter to define a &quot;linked&quot; primer - see https://cutadapt.readthedocs.io for complete details." title="adapter_f: List[Str]">
                <param name="element" type="text" label="element: Str" help="[required]">
                    <sanitizer>
                        <valid initial="string.printable"/>
                    </sanitizer>