Mercurial > repos > q2d2 > qiime2__rescript__orient_reads

changeset 0:d9ed903baa9a draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit b1fccfb38b4873cd4699743033449014a2978e7d
author q2d2
date Mon, 05 May 2025 19:02:25 +0000
parents
children
files qiime2__rescript__orient_reads.xml test-data/.gitkeep
diffstat 1 files changed, 80 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__orient_reads.xml	Mon May 05 19:02:25 2025 +0000
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+<?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 orient-reads" id="qiime2__rescript__orient_reads" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
+    <description>Orient FASTQ reads against reference.</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 orient_reads '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="sequences" type="data" format="qza" label="sequences: SampleData[PairedEndSequencesWithQuality¹ | JoinedSequencesWithQuality²]" help="[required]  Sequence reads to be oriented.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
+                <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[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]']</validator>
+        </param>
+        <param name="reference_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required]  Reference sequences to orient against.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <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="dbmask" type="select" label="dbmask: Str % Choices('none', 'dust', 'soft')" display="radio">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="none">none</option>
+                <option value="dust">dust</option>
+                <option value="soft">soft</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="oriented_reads" format="qza" label="${tool.name} on ${on_string}: oriented_reads.qza" from_work_dir="oriented_reads.qza"/>
+        <data name="unmatched_reads" format="qza" label="${tool.name} on ${on_string}: unmatched_reads.qza" from_work_dir="unmatched_reads.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript orient-reads
+==============================
+Orient FASTQ reads against reference.
+
+
+Outputs:
+--------
+:oriented_reads.qza: Oriented reads.
+:unmatched_reads.qza: Reads that fail to match at least one reference sequence in either + or - orientation.
+
+|  
+
+Description:
+------------
+Orient input reads (FASTQ) by comparison against a set of reference sequences using VSEARCH. This action is useful for orienting reads that are in mixed orientations prior to denoising or clustering.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.7717/peerj.2584</citation>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>