changeset 2:0eb4a44e8395 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

--- a/qiime2__vsearch__merge_pairs.xml	Thu Jun 08 19:53:10 2023 +0000
+++ b/qiime2__vsearch__merge_pairs.xml	Thu Apr 25 21:27:33 2024 +0000
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+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: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 vsearch merge-pairs" id="qiime2__vsearch__merge_pairs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 vsearch merge-pairs" id="qiime2__vsearch__merge_pairs" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Merge paired-end reads.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</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"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </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.">
@@ -32,16 +32,16 @@
             <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="minovlen" type="integer" min="5" value="10" label="minovlen: Int % Range(5, 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 ${on_string}: merged_sequences.qza" from_work_dir="merged_sequences.qza"/>
+        <data name="unmerged_sequences" format="qza" label="${tool.name} on ${on_string}: unmerged_sequences.qza" from_work_dir="unmerged_sequences.qza"/>
     </outputs>
     <tests/>
     <help>
@@ -53,6 +53,7 @@
 Outputs:
 --------
 :merged_sequences.qza: The merged sequences.
+:unmerged_sequences.qza: The unmerged paired-end reads.
 
 |