changeset 0:b26cb5419c39 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 69da7976573cc07a363ac66bdacc9269d7cd3732

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__vsearch__merge_pairs.xml	Fri Jan 13 23:01:44 2023 +0000
@@ -0,0 +1,71 @@
+<?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: 2022.11.1)
+for:
+    qiime2 (version: 2022.11.1)
+-->
+<tool name="qiime2 vsearch merge-pairs" id="qiime2__vsearch__merge_pairs" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Merge paired-end reads.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
+    </requirements>
+    <version_command>q2galaxy version vsearch</version_command>
+    <command detect_errors="exit_code">q2galaxy run vsearch merge_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 merged.">
+            <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 merging of staggered read pairs."/>
+            <param name="minovlen" type="integer" min="0" value="10" label="minovlen: Int % Range(0, None)" help="[default: 10]  Minimum length of the area of overlap between reads during merging."/>
+            <param name="maxdiffs" type="integer" min="0" value="10" label="maxdiffs: Int % Range(0, None)" help="[default: 10]  Maximum number of mismatches in the area of overlap during merging."/>
+            <param name="minmergelen" type="integer" min="0" optional="true" label="minmergelen: Int % Range(0, None)" help="[optional]  Minimum length of the merged 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 merged 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 merged 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="merged_sequences" format="qza" label="${tool.name} on ${on_string}: merged_sequences.qza" from_work_dir="merged_sequences.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: vsearch merge-pairs
+============================
+Merge paired-end reads.
+
+
+Outputs:
+--------
+:merged_sequences.qza: The merged sequences.
+
+|  
+
+Description:
+------------
+Merge paired-end sequence reads using vsearch's merge_pairs function. See the vsearch documentation for details on how paired-end merging 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>