comparison qiime2__cutadapt__demux_paired.xml @ 3:f21509fa9ed0 draft

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

2:c6a8822e19f2

<?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 demux-paired" id="qiime2__cutadapt__demux_paired" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Demultiplex paired-end sequence data with barcodes in-sequence.</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 demux_paired '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required]  The paired-end sequences to be demultiplexed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/>

                    <param name="column" type="text" label="Column Name">
                        <validator type="empty_field"/>
                    </param>
                </when>
            </conditional>
            <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]  The level of error tolerance, specified as the maximum allowable error rate."/>
            <param name="batch_size" type="integer" min="0" value="0" label="batch_size: Int % Range(0, None)" help="[default: 0]  The number of samples cutadapt demultiplexes concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; to process all samples at once."/>
            <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1]  Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/>
            <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No]  Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/>
            <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1]  Number of CPU cores to use."/>
        </section>
    </inputs>
    <outputs>
        <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
        <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>

3:f21509fa9ed0

<?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 demux-paired" id="qiime2__cutadapt__demux_paired" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Demultiplex paired-end sequence data with barcodes in-sequence.</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 demux_paired '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required]  The paired-end sequences to be demultiplexed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/>

                    <param name="column" type="text" label="Column Name">
                        <validator type="empty_field"/>
                    </param>
                </when>
            </conditional>
            <param name="forward_cut" type="integer" value="0" label="forward_cut: Int" help="[default: 0]  Remove the specified number of bases from the forward sequences. Bases are removed before demultiplexing. If a positive value is provided, bases are removed from the beginning of the sequences. If a negative value is provided, bases are removed from the end of the sequences. If --p-mixed-orientation is set, then both --p-forward-cut and --p-reverse-cut must be set to the same value."/>
            <param name="reverse_cut" type="integer" value="0" label="reverse_cut: Int" help="[default: 0]  Remove the specified number of bases from the reverse sequences. Bases are removed before demultiplexing. If a positive value is provided, bases are removed from the beginning of the sequences. If a negative value is provided, bases are removed from the end of the sequences. If --p-mixed-orientation is set, then both --p-forward-cut and --p-reverse-cut must be set to the same value."/>
            <param name="anchor_forward_barcode" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="anchor_forward_barcode: Bool" help="[default: No]  Anchor the forward barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the forward sequence. Can speed up demultiplexing if used."/>
            <param name="anchor_reverse_barcode" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="anchor_reverse_barcode: Bool" help="[default: No]  Anchor the reverse barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the reverse sequence. Can speed up demultiplexing if used."/>
            <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]  The level of error tolerance, specified as the maximum allowable error rate."/>
            <param name="batch_size" type="integer" min="0" value="0" label="batch_size: Int % Range(0, None)" help="[default: 0]  The number of samples cutadapt demultiplexes concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; to process all samples at once."/>
            <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1]  Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/>
            <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No]  Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/>
        </section>
    </inputs>
    <outputs>
        <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
        <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>