# HG changeset patch
# User q2d2
# Date 1661802034 0
# Node ID 7330b10c19a70a8bc5eeb6307279967dfba1b466

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 7330b10c19a7 qiime2__diversity_lib__bray_curtis.xml
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+++ b/qiime2__diversity_lib__bray_curtis.xml	Mon Aug 29 19:40:34 2022 +0000
@@ -0,0 +1,185 @@
+<?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-lib bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Bray-Curtis Dissimilarity</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version diversity_lib</version_command>
+    <command detect_errors="aggressive">q2galaxy run diversity_lib bray_curtis '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.">
+            <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">
+            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.">
+                    <option value="auto">auto (Str)</option>
+                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
+                </param>
+                <when value="auto">
+                    <param name="n_jobs" type="hidden" value="auto"/>
+                </when>
+                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
+                    <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1]  The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="bray_curtis.test0.feature-table.qza" ftype="qza"/>
+            <output name="distance_matrix" ftype="qza">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: DistanceMatrix"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
+            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
+                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
+                <param name="n_jobs" value="1"/>
+            </conditional>
+            <output name="distance_matrix" ftype="qza">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: DistanceMatrix"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
+            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
+                <param name="__q2galaxy__GUI__select__" value="auto"/>
+                <param name="n_jobs" value="auto"/>
+            </conditional>
+            <output name="distance_matrix" ftype="qza">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: DistanceMatrix"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+QIIME 2: diversity-lib bray-curtis
+==================================
+Bray-Curtis Dissimilarity
+
+
+Outputs:
+--------
+:distance_matrix.qza: Distance matrix for Bray-Curtis dissimilarity
+
+|  
+
+Description:
+------------
+Compute Bray-Curtis dissimilarity for each sample in a feature table. Note: Frequency and relative frequency data produce different results unless overall sample sizes are identical. Please consider the impact on your results if you use Bray-Curtis with count data that has not been adjusted (normalized).
+
+Examples:
+---------
+
+run on one core (by default)
+****************************
+Using the ``qiime2 diversity-lib bray-curtis`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
+      - ``bray-curtis-dm.qza``
+
+to run on n cores, replace 1 here with your preferred integer
+*************************************************************
+Using the ``qiime2 diversity-lib bray-curtis`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Expand the ``additional options`` section
+
+    - Leave *"n_jobs"* as its default value of ``1``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
+      - ``bray-curtis-dm.qza``
+
+use 'auto' to run on all of host system's available CPU cores
+*************************************************************
+Using the ``qiime2 diversity-lib bray-curtis`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Expand the ``additional options`` section
+
+    - Set *"n_jobs"* to ``auto``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 diversity-lib bray-curtis [...] : distance_matrix.qza``
+      - ``bray-curtis-dm.qza``
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="bibtex">@article{cite1,
+ author = {Sørensen, Thorvald},
+ journal = {Biol. Skr.},
+ pages = {1--34},
+ title = {A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
+ volume = {5},
+ year = {1948}
+}
+</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
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