Mercurial > repos > q2d2 > qiime2vsearchjoin_pairs

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+++ b/qiime2__vsearch__join_pairs.xml	Mon Aug 29 20:33:27 2022 +0000
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+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, 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: 2022.8.1)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 vsearch join-pairs" id="qiime2__vsearch__join_pairs" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Join paired-end reads.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version vsearch</version_command>
+    <command detect_errors="aggressive">q2galaxy run vsearch join_pairs '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[PairedEndSequencesWithQuality]" help="[required]  The demultiplexed paired-end sequences to be joined.">
+            <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="truncqual" type="integer" min="0" optional="true" label="truncqual: Int % Range(0, None)" help="[optional]  Truncate sequences at the first base with the specified quality score value or lower."/>
+            <param name="minlen" type="integer" min="0" value="1" label="minlen: Int % Range(0, None)" help="[default: 1]  Sequences shorter than minlen after truncation are discarded."/>
+            <param name="maxns" type="integer" min="0" optional="true" label="maxns: Int % Range(0, None)" help="[optional]  Sequences with more than maxns N characters are discarded."/>
+            <param name="allowmergestagger" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allowmergestagger: Bool" help="[default: No]  Allow joining of staggered read pairs."/>
+            <param name="minovlen" type="integer" min="0" value="10" label="minovlen: Int % Range(0, None)" help="[default: 10]  Minimum overlap length of forward and reverse reads for joining."/>
+            <param name="maxdiffs" type="integer" min="0" value="10" label="maxdiffs: Int % Range(0, None)" help="[default: 10]  Maximum number of mismatches in the forward/reverse read overlap for joining."/>
+            <param name="minmergelen" type="integer" min="0" optional="true" label="minmergelen: Int % Range(0, None)" help="[optional]  Minimum length of the joined read to be retained."/>
+            <param name="maxmergelen" type="integer" min="0" optional="true" label="maxmergelen: Int % Range(0, None)" help="[optional]  Maximum length of the joined read to be retained."/>
+            <param name="maxee" type="float" min="0.0" optional="true" label="maxee: Float % Range(0.0, None)" help="[optional]  Maximum number of expected errors in the joined read to be retained."/>
+            <param name="threads" type="integer" min="0" max="8" value="1" label="threads: Int % Range(0, 8, inclusive_end=True)" help="[default: 1]  The number of threads to use for computation. Does not scale much past 4 threads."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="joined_sequences" format="qza" label="${tool.name} on ${on_string}: joined_sequences.qza" from_work_dir="joined_sequences.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: vsearch join-pairs
+===========================
+Join paired-end reads.
+
+
+Outputs:
+--------
+:joined_sequences.qza: The joined sequences.
+
+|
+
+Description:
+------------
+Join paired-end sequence reads using vsearch's merge_pairs function. See the vsearch documentation for details on how paired-end joining is performed, and for more information on the parameters to this method.
+
+
+|
+
+</help>
+    <citations>
+        <citation type="doi">10.7717/peerj.2584</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>