comparison qiime2__rescript__extract_seq_segments.xml @ 3:80a749825bfd draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit b1fccfb38b4873cd4699743033449014a2978e7d

2:8d441435b9e6

<?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 rescript extract-seq-segments" id="qiime2__rescript__extract_seq_segments" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.</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 rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript extract_seq_segments '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>

            <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="perc_identity" type="float" min="1e-06" max="1" value="0.7" label="perc_identity: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.7]  The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter."/>
            <param name="target_coverage" type="float" min="1e-06" max="1" value="0.9" label="target_coverage: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.9]  The minimum fraction of coverage that 'reference-segment-sequences' must have in order to extract matching segments from 'input-sequences'."/>
            <param name="min_seq_len" type="integer" min="1" optional="true" label="min_seq_len: Int % Range(1, None)" help="[optional]  Minimum length of sequence allowed for searching. Any sequence less than this will be discarded. If not set, default program settings will be used."/>
            <param name="threads" type="integer" min="1" max="255" value="1" label="threads: Int % Range(1, 256)" help="[default: 1]  Number of computation threads to use (1 to 256). The number of threads should be lesser or equal to the number of available CPU cores."/>
        </section>
    </inputs>
    <outputs>
        <data name="extracted_sequence_segments" format="qza" label="${tool.name} on ${on_string}: extracted_sequence_segments.qza" from_work_dir="extracted_sequence_segments.qza"/>

3:80a749825bfd

<?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 rescript extract-seq-segments" id="qiime2__rescript__extract_seq_segments" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined 'perc-identity' value.</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 rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript extract_seq_segments '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>

            <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="perc_identity" type="float" min="1e-06" max="1" value="0.7" label="perc_identity: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.7]  The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter."/>
            <param name="target_coverage" type="float" min="1e-06" max="1" value="0.9" label="target_coverage: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 0.9]  The minimum fraction of coverage that 'reference-segment-sequences' must have in order to extract matching segments from 'input-sequences'."/>
            <param name="min_seq_len" type="integer" min="1" value="32" label="min_seq_len: Int % Range(1, None)" help="[default: 32]  Minimum length of reference sequence segment allowed for searching. Any sequence less than this will be discarded."/>
            <param name="max_seq_len" type="integer" min="1" value="50000" label="max_seq_len: Int % Range(1, None)" help="[default: 50000]  Maximum length of reference sequence segment allowed for searching. Any sequence greater than this will be discarded."/>
            <param name="threads" type="integer" min="1" max="255" value="1" label="threads: Int % Range(1, 256)" help="[default: 1]  Number of computation threads to use (1 to 256). The number of threads should be lesser or equal to the number of available CPU cores."/>
        </section>
    </inputs>
    <outputs>
        <data name="extracted_sequence_segments" format="qza" label="${tool.name} on ${on_string}: extracted_sequence_segments.qza" from_work_dir="extracted_sequence_segments.qza"/>