# HG changeset patch
# User q2d2
# Date 1686253875 0
# Node ID 2e8e3258af39f618a2a5d2f7d31d57e43f00d5b9

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556

diff -r 000000000000 -r 2e8e3258af39 qiime2__quality_control__decontam_remove.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__quality_control__decontam_remove.xml	Thu Jun 08 19:51:15 2023 +0000
@@ -0,0 +1,67 @@
+<?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: 2023.5.0)
+for:
+    qiime2 (version: 2023.5.1)
+-->
+<tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+    <description>Removes contaminant</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2023.5</container>
+    </requirements>
+    <version_command>q2galaxy version quality_control</version_command>
+    <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required]  Output table from decontam identify">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[DecontamScore]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]']</validator>
+        </param>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  ASV or OTU table which contaminate sequences will be identified from">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="threshold" type="float" value="0.1" label="threshold: Float" help="[default: 0.1]  Select threshold cutoff for decontam algorithm scores"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: quality-control decontam-remove
+========================================
+Removes contaminant
+
+
+Outputs:
+--------
+:filtered_table.qza: The resulting feature table of scores once contaminants are removed
+
+|  
+
+Description:
+------------
+This method removes contaminant sequences from an OTU or ASV table and returns the amended table to the user
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 2e8e3258af39 test-data/.gitkeep