diff qiime2__cutadapt__trim_paired.xml @ 1:4f340404bbf8 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732

--- a/qiime2__cutadapt__trim_paired.xml	Mon Aug 29 19:21:23 2022 +0000
+++ b/qiime2__cutadapt__trim_paired.xml	Fri Jan 13 22:41:40 2023 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+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: 2022.8.1)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
     <version_command>q2galaxy version cutadapt</version_command>
-    <command detect_errors="aggressive">q2galaxy run cutadapt trim_paired '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -85,6 +85,11 @@
             <param name="match_adapter_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="match_adapter_wildcards: Bool" help="[default: Yes]  Interpret IUPAC wildcards (e.g., N) in adapters."/>
             <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1]  Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/>
             <param name="discard_untrimmed" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="discard_untrimmed: Bool" help="[default: No]  Discard reads in which no adapter was found."/>
+            <param name="max_expected_errors" type="float" min="0" optional="true" label="max_expected_errors: Float % Range(0, None)" help="[optional]  Discard reads that exceed maximum expected erroneous nucleotides."/>
+            <param name="max_n" type="float" min="0" optional="true" label="max_n: Float % Range(0, None)" help="[optional]  Discard reads with more than COUNT N bases. If COUNT_or_FRACTION is a number between 0 and 1, it is interpreted as a fraction of the read length."/>
+            <param name="quality_cutoff_5end" type="integer" min="0" value="0" label="quality_cutoff_5end: Int % Range(0, None)" help="[default: 0]  Trim nucleotides with Phred score quality lower than threshold from 5 prime end."/>
+            <param name="quality_cutoff_3end" type="integer" min="0" value="0" label="quality_cutoff_3end: Int % Range(0, None)" help="[default: 0]  Trim nucleotides with Phred score quality lower than threshold from 3 prime end."/>
+            <param name="quality_base" type="integer" min="0" value="33" label="quality_base: Int % Range(0, None)" help="[default: 33]  How the Phred score is encoded (33 or 64)."/>
         </section>
     </inputs>
     <outputs>