# HG changeset patch
# User q2d2
# Date 1661802335 0
# Node ID da97d578001c22fe84ce63bd00b315f8178cad0a

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

diff -r 000000000000 -r da97d578001c qiime2__diversity_lib__beta_passthrough.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__diversity_lib__beta_passthrough.xml	Mon Aug 29 19:45:35 2022 +0000
@@ -0,0 +1,249 @@
+<?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 beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Beta Passthrough (non-phylogenetic)</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 beta_passthrough '$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 over which beta diversity 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>
+        <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jensenshannon', 'kulsinski', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')">
+            <option value="__q2galaxy__::literal::None">Selection required</option>
+            <option value="aitchison">aitchison</option>
+            <option value="canberra">canberra</option>
+            <option value="canberra_adkins">canberra_adkins</option>
+            <option value="chebyshev">chebyshev</option>
+            <option value="cityblock">cityblock</option>
+            <option value="correlation">correlation</option>
+            <option value="cosine">cosine</option>
+            <option value="dice">dice</option>
+            <option value="euclidean">euclidean</option>
+            <option value="hamming">hamming</option>
+            <option value="jensenshannon">jensenshannon</option>
+            <option value="kulsinski">kulsinski</option>
+            <option value="matching">matching</option>
+            <option value="minkowski">minkowski</option>
+            <option value="rogerstanimoto">rogerstanimoto</option>
+            <option value="russellrao">russellrao</option>
+            <option value="seuclidean">seuclidean</option>
+            <option value="sokalmichener">sokalmichener</option>
+            <option value="sokalsneath">sokalsneath</option>
+            <option value="sqeuclidean">sqeuclidean</option>
+            <option value="yule">yule</option>
+            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1]  A pseudocount to handle zeros for compositional metrics. This is ignored for non-compositional metrics."/>
+            <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="beta_passthrough.test0.feature-table.qza" ftype="qza"/>
+            <param name="metric" value="euclidean"/>
+            <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="beta_passthrough.test1.feature-table.qza" ftype="qza"/>
+            <param name="metric" value="kulsinski"/>
+            <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="beta_passthrough.test2.feature-table.qza" ftype="qza"/>
+            <param name="metric" value="aitchison"/>
+            <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>
+        <test>
+            <param name="table" value="beta_passthrough.test3.feature-table.qza" ftype="qza"/>
+            <param name="metric" value="aitchison"/>
+            <param name="pseudocount" value="5"/>
+            <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 beta-passthrough
+=======================================
+Beta Passthrough (non-phylogenetic)
+
+
+Outputs:
+--------
+:distance_matrix.qza: The resulting distance matrix.
+
+|  
+
+Description:
+------------
+Computes a distance matrix for all pairs of samples in a feature table using the scikit-bio implementation of the selected beta diversity metric.
+
+Examples:
+---------
+
+run on one core (by default)
+****************************
+Using the ``qiime2 diversity-lib beta-passthrough`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Set *"metric"* to ``euclidean``
+ #. 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 beta-passthrough [...] : distance_matrix.qza``
+      - ``euclidean-dm.qza``
+
+to run on n cores, replace 1 here with your preferred integer
+*************************************************************
+Using the ``qiime2 diversity-lib beta-passthrough`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Set *"metric"* to ``kulsinski``
+ #. 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 beta-passthrough [...] : distance_matrix.qza``
+      - ``kulsinski-dm.qza``
+
+use 'auto' to run on all of host system's available CPU cores
+*************************************************************
+| A default pseudocount of 1 is added to feature counts. Pseudocount is ignored for non-compositional metrics.
+Using the ``qiime2 diversity-lib beta-passthrough`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Set *"metric"* to ``aitchison``
+ #. 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 beta-passthrough [...] : distance_matrix.qza``
+      - ``aitchison-dm.qza``
+
+use 'pseudocount' to manually set a pseudocount for compositional metrics
+*************************************************************************
+Using the ``qiime2 diversity-lib beta-passthrough`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Set *"metric"* to ``aitchison``
+ #. Expand the ``additional options`` section
+
+    #. Set *"pseudocount"* to ``5``
+    #. 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 beta-passthrough [...] : distance_matrix.qza``
+      - ``aitchison-dm.qza``
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r da97d578001c test-data/alpha_passthrough.test0.feature-table.qza
Binary file test-data/alpha_passthrough.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_passthrough.test0.feature-table.qza
Binary file test-data/beta_passthrough.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_passthrough.test1.feature-table.qza
Binary file test-data/beta_passthrough.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_passthrough.test2.feature-table.qza
Binary file test-data/beta_passthrough.test2.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_passthrough.test3.feature-table.qza
Binary file test-data/beta_passthrough.test3.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test0.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test1.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test2.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test2.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test3.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test3.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test4.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test4.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test5.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test5.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test6.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test6.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/bray_curtis.test0.feature-table.qza
Binary file test-data/bray_curtis.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/bray_curtis.test1.feature-table.qza
Binary file test-data/bray_curtis.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/bray_curtis.test2.feature-table.qza
Binary file test-data/bray_curtis.test2.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/faith_pd.test0.feature-table.qza
Binary file test-data/faith_pd.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/faith_pd.test0.phylogeny.qza
Binary file test-data/faith_pd.test0.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/jaccard.test0.feature-table.qza
Binary file test-data/jaccard.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/jaccard.test1.feature-table.qza
Binary file test-data/jaccard.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/jaccard.test2.feature-table.qza
Binary file test-data/jaccard.test2.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/observed_features.test0.feature-table.qza
Binary file test-data/observed_features.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/pielou_evenness.test0.feature-table.qza
Binary file test-data/pielou_evenness.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/pielou_evenness.test1.feature-table.qza
Binary file test-data/pielou_evenness.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/shannon_entropy.test0.feature-table.qza
Binary file test-data/shannon_entropy.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/shannon_entropy.test1.feature-table.qza
Binary file test-data/shannon_entropy.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test0.feature-table.qza
Binary file test-data/unweighted_unifrac.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test0.phylogeny.qza
Binary file test-data/unweighted_unifrac.test0.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test1.feature-table.qza
Binary file test-data/unweighted_unifrac.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test1.phylogeny.qza
Binary file test-data/unweighted_unifrac.test1.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test2.feature-table.qza
Binary file test-data/unweighted_unifrac.test2.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test2.phylogeny.qza
Binary file test-data/unweighted_unifrac.test2.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test3.feature-table.qza
Binary file test-data/unweighted_unifrac.test3.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/unweighted_unifrac.test3.phylogeny.qza
Binary file test-data/unweighted_unifrac.test3.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test0.feature-table.qza
Binary file test-data/weighted_unifrac.test0.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test0.phylogeny.qza
Binary file test-data/weighted_unifrac.test0.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test1.feature-table.qza
Binary file test-data/weighted_unifrac.test1.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test1.phylogeny.qza
Binary file test-data/weighted_unifrac.test1.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test2.feature-table.qza
Binary file test-data/weighted_unifrac.test2.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test2.phylogeny.qza
Binary file test-data/weighted_unifrac.test2.phylogeny.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test3.feature-table.qza
Binary file test-data/weighted_unifrac.test3.feature-table.qza has changed
diff -r 000000000000 -r da97d578001c test-data/weighted_unifrac.test3.phylogeny.qza
Binary file test-data/weighted_unifrac.test3.phylogeny.qza has changed