changeset 0:2dcfb3ea0e51 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__diversity__beta_correlation.xml	Mon Aug 29 19:34:16 2022 +0000
@@ -0,0 +1,96 @@
+<?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 diversity beta-correlation" id="qiime2__diversity__beta_correlation" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Beta diversity correlation</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version diversity</version_command>
+    <command detect_errors="aggressive">q2galaxy run diversity beta_correlation '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required]  Matrix of distances between pairs of samples.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="DistanceMatrix"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['DistanceMatrix']</validator>
+        </param>
+        <conditional name="metadata">
+            <param name="type" type="select" label="metadata: MetadataColumn[Numeric]" help="[required]  Numeric metadata column from which to compute pairwise Euclidean distances">
+                <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"/>
+                <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
+                    <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
+                </param>
+            </when>
+            <when value="qza">
+                <param name="source" type="data" format="qza" label="Metadata Source"/>
+                <param name="column" type="text" label="Column Name">
+                    <validator type="empty_field"/>
+                </param>
+            </when>
+        </conditional>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="method" type="select" label="method: Str % Choices('spearman', 'pearson')" display="radio">
+                <option value="spearman" selected="true">spearman</option>
+                <option value="pearson">pearson</option>
+            </param>
+            <param name="permutations" type="integer" min="0" value="999" label="permutations: Int % Range(0, None)" help="[default: 999]  The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/>
+            <param name="intersect_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="intersect_ids: Bool" help="[default: No]  If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs."/>
+            <param name="label1" type="text" value="Metadata" label="label1: Str" help="[default: 'Metadata']  Label for `distance_matrix` in the output visualization.">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="label2" type="text" value="Distance Matrix" label="label2: Str" help="[default: 'Distance Matrix']  Label for `metadata_distance_matrix` in the output visualization.">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="metadata_distance_matrix" format="qza" label="${tool.name} on ${on_string}: metadata_distance_matrix.qza" from_work_dir="metadata_distance_matrix.qza"/>
+        <data name="mantel_scatter_visualization" format="qzv" label="${tool.name} on ${on_string}: mantel_scatter_visualization.qzv" from_work_dir="mantel_scatter_visualization.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: diversity beta-correlation
+===================================
+Beta diversity correlation
+
+
+Outputs:
+--------
+:metadata_distance_matrix.qza: The Distance Matrix produced from the metadata column and used in the mantel test
+:mantel_scatter_visualization.qzv: Scatter plot rendering of the manteltest results
+
+|  
+
+Description:
+------------
+Create a distance matrix from a numeric metadata column and apply a two-sided Mantel test to identify correlation between two distance matrices. Actions used internally: `distance-matrix` from q2-metadata and `mantel` from q2-diversity.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>