# HG changeset patch
# User q2d2
# Date 1686253860 0
# Node ID ba52336465f9d74ad260bf21dd9d1c3228672cf3

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

diff -r 000000000000 -r ba52336465f9 qiime2__quality_control__decontam_identify.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__quality_control__decontam_identify.xml	Thu Jun 08 19:51:00 2023 +0000
@@ -0,0 +1,127 @@
+<?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-identify" id="qiime2__quality_control__decontam_identify" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+    <description>Identify contaminants</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_identify '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </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">
+            <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>
+        <repeat name="metadata" min="1" help="[required]  metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter" title="metadata: Metadata">
+            <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                <param name="type" type="select" label="metadata: Metadata">
+                    <option value="tsv" selected="true">Metadata from TSV</option>
+                    <option value="qza">Metadata from Artifact</option>
+                </param>
+                <when value="tsv">
+                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                </when>
+                <when value="qza">
+                    <param name="source" type="data" format="qza" label="Metadata Source"/>
+                </when>
+            </conditional>
+        </repeat>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="method" type="select" label="method: Str % Choices('combined', 'frequency', 'prevalence')" display="radio">
+                <option value="combined">combined</option>
+                <option value="frequency">frequency</option>
+                <option value="prevalence" selected="true">prevalence</option>
+            </param>
+            <conditional name="__q2galaxy__GUI__conditional__freq_concentration_column__" label="freq_concentration_column: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="freq_concentration_column: Str" help="[optional]  Input column name that has concentration information for the samples">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="freq_concentration_column" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="freq_concentration_column" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__prev_control_column__" label="prev_control_column: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_column: Str" help="[optional]  Input column name containing experimental or control sample metadata">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="prev_control_column" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="prev_control_column" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__prev_control_indicator__" label="prev_control_indicator: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_indicator: Str" help="[optional]  indicate the control sample identifier (e.g. &quot;control&quot; or &quot;blank&quot;)">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="prev_control_indicator" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="prev_control_indicator" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="decontam_scores" format="qza" label="${tool.name} on ${on_string}: decontam_scores.qza" from_work_dir="decontam_scores.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: quality-control decontam-identify
+==========================================
+Identify contaminants
+
+
+Outputs:
+--------
+: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
+
+|  
+
+Description:
+------------
+This method identifies contaminant sequences from an OTU or ASV table and reports them to the user
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r ba52336465f9 test-data/.gitkeep