# HG changeset patch
# User q2d2
# Date 1717457417 0
# Node ID 1c23691fa0c5132c27aa9c500bcc8862f33c0db9
# Parent  2c425b0e5cdbc4b96edbab8c04fcc893a83a7583
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit c7e80dcda727ce63b42aa8a946e9330310929797

diff -r 2c425b0e5cdb -r 1c23691fa0c5 qiime2__quality_control__decontam_identify_batches.xml
--- a/qiime2__quality_control__decontam_identify_batches.xml	Thu Apr 25 21:18:00 2024 +0000
+++ b/qiime2__quality_control__decontam_identify_batches.xml	Mon Jun 03 23:30:17 2024 +0000
@@ -6,14 +6,14 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2024.2.1)
+    q2galaxy (version: 2024.5.0)
 for:
-    qiime2 (version: 2024.2.0)
+    qiime2 (version: 2024.5.0)
 -->
-<tool name="qiime2 quality-control decontam-identify-batches" id="qiime2__quality_control__decontam_identify_batches" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 quality-control decontam-identify-batches" id="qiime2__quality_control__decontam_identify_batches" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
     <description>Identify contaminants in Batch Mode</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
     </requirements>
     <version_command>q2galaxy version quality_control</version_command>
     <command detect_errors="exit_code">q2galaxy run quality_control decontam_identify_batches '$inputs'</command>
@@ -21,7 +21,7 @@
         <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
-        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  ASV or OTU table which contaminate sequences will be identified from">
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table which contaminate sequences will be identified from">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
             </options>
@@ -55,6 +55,12 @@
             <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="rep_seqs" type="data" format="qza" optional="true" label="rep_seqs: FeatureData[Sequence]" help="[optional]  Representative Sequences table which contaminate seqeunces will be removed from">
+                <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>
             <param name="filter_empty_features" type="select" label="filter_empty_features: Bool" help="[optional]  If true, features which are not present in a split feature table are dropped." display="radio">
                 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
                 <option value="__q2galaxy__::literal::True">Yes</option>
@@ -132,7 +138,7 @@
 Outputs:
 --------
 :batch_subset_tables.qza: Directory where feature tables split based on metadata and parameter split_column values should be written.
-:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each ASV or OTU on how likely they are to be a contaminant sequence
+:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence
 :score_histograms.qzv: The vizulaizer histograms for all decontam score objects generated from the pipeline
 
 |