# HG changeset patch
# User q2d2
# Date 1661802905 0
# Node ID e2b704eca81516eeca7e034cc7f60eac9bf4b246

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r e2b704eca815 qiime2__feature_table__filter_samples.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_table__filter_samples.xml	Mon Aug 29 19:55:05 2022 +0000
@@ -0,0 +1,99 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, 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)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Filter samples from table</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version feature_table</version_command>
+    <command detect_errors="aggressive">q2galaxy run feature_table filter_samples '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required]  The feature table from which samples should be filtered.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Composition]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="min_frequency" type="integer" value="0" label="min_frequency: Int" help="[default: 0]  The minimum total frequency that a sample must have to be retained."/>
+            <param name="max_frequency" type="integer" optional="true" label="max_frequency: Int" help="[optional]  The maximum total frequency that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum frequency filter will be applied)."/>
+            <param name="min_features" type="integer" value="0" label="min_features: Int" help="[default: 0]  The minimum number of features that a sample must have to be retained."/>
+            <param name="max_features" type="integer" optional="true" label="max_features: Int" help="[optional]  The maximum number of features that a sample can have to be retained. If no value is provided this will default to infinity (i.e., no maximum feature filter will be applied)."/>
+            <repeat name="metadata" help="[optional]  Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude_ids` when selecting samples to discard." 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>
+            <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional]  SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained.">
+                    <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="where" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="where" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No]  If true, the samples selected by `metadata` or `where` parameters will be excluded from the filtered table instead of being retained."/>
+            <param name="filter_empty_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="filter_empty_features: Bool" help="[default: Yes]  If true, features which are not present in any retained samples are dropped."/>
+        </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: feature-table filter-samples
+=====================================
+Filter samples from table
+
+
+Outputs:
+--------
+:filtered_table.qza: The resulting feature table filtered by sample.
+
+|  
+
+Description:
+------------
+Filter samples from table based on frequency and/or metadata. Any features with a frequency of zero after sample filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
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