Repository 'qiime2__diversity_lib__beta_phylogenetic_passthrough'
hg clone https://toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__diversity_lib__beta_phylogenetic_passthrough

Changeset 3:a1166fa9986e (2024-04-25)
Previous changeset 2:fcbeb4dc4b81 (2023-06-08) Next changeset 4:2be808ff0cd2 (2024-06-03)
Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
modified:
qiime2__diversity_lib__beta_phylogenetic_passthrough.xml
test-data/alpha_passthrough.test0.feature-table.qza
test-data/beta_passthrough.test0.feature-table.qza
test-data/beta_passthrough.test1.feature-table.qza
test-data/beta_passthrough.test2.feature-table.qza
test-data/beta_passthrough.test3.feature-table.qza
test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza
test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza
test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza
test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza
test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza
test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza
test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza
test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza
test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza
test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza
test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza
test-data/beta_phylogenetic_passthrough.test0.feature-table.qza
test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza
test-data/beta_phylogenetic_passthrough.test1.feature-table.qza
test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza
test-data/beta_phylogenetic_passthrough.test2.feature-table.qza
test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza
test-data/beta_phylogenetic_passthrough.test3.feature-table.qza
test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza
test-data/beta_phylogenetic_passthrough.test4.feature-table.qza
test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza
test-data/beta_phylogenetic_passthrough.test5.feature-table.qza
test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza
test-data/beta_phylogenetic_passthrough.test6.feature-table.qza
test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza
test-data/bray_curtis.test0.feature-table.qza
test-data/bray_curtis.test1.feature-table.qza
test-data/bray_curtis.test2.feature-table.qza
test-data/faith_pd.test0.feature-table.qza
test-data/faith_pd.test0.phylogeny.qza
test-data/jaccard.test0.feature-table.qza
test-data/jaccard.test1.feature-table.qza
test-data/jaccard.test2.feature-table.qza
test-data/observed_features.test0.feature-table.qza
test-data/pielou_evenness.test0.feature-table.qza
test-data/pielou_evenness.test1.feature-table.qza
test-data/shannon_entropy.test0.feature-table.qza
test-data/shannon_entropy.test1.feature-table.qza
test-data/unweighted_unifrac.test0.feature-table.qza
test-data/unweighted_unifrac.test0.phylogeny.qza
test-data/unweighted_unifrac.test1.feature-table.qza
test-data/unweighted_unifrac.test1.phylogeny.qza
test-data/unweighted_unifrac.test2.feature-table.qza
test-data/unweighted_unifrac.test2.phylogeny.qza
test-data/unweighted_unifrac.test3.feature-table.qza
test-data/unweighted_unifrac.test3.phylogeny.qza
test-data/weighted_unifrac.test0.feature-table.qza
test-data/weighted_unifrac.test0.phylogeny.qza
test-data/weighted_unifrac.test1.feature-table.qza
test-data/weighted_unifrac.test1.phylogeny.qza
test-data/weighted_unifrac.test2.feature-table.qza
test-data/weighted_unifrac.test2.phylogeny.qza
test-data/weighted_unifrac.test3.feature-table.qza
test-data/weighted_unifrac.test3.phylogeny.qza
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diff -r fcbeb4dc4b81 -r a1166fa9986e qiime2__diversity_lib__beta_phylogenetic_passthrough.xml
--- a/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml Thu Jun 08 19:38:53 2023 +0000
+++ b/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml Thu Apr 25 21:01:00 2024 +0000
[
b'@@ -1,24 +1,24 @@\n <?xml version=\'1.0\' encoding=\'utf-8\'?>\n <!--\n-Copyright (c) 2023, QIIME 2 development team.\n+Copyright (c) 2024, QIIME 2 development team.\n \n Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)\n -->\n <!--\n This tool was automatically generated by:\n-    q2galaxy (version: 2023.5.0)\n+    q2galaxy (version: 2024.2.1)\n for:\n-    qiime2 (version: 2023.5.1)\n+    qiime2 (version: 2024.2.0)\n -->\n-<tool name="qiime2 diversity-lib beta-phylogenetic-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">\n+<tool name="qiime2 diversity-lib beta-phylogenetic-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_passthrough" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">\n     <description>Beta Phylogenetic Passthrough</description>\n     <requirements>\n-        <container type="docker">quay.io/qiime2/core:2023.5</container>\n+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>\n     </requirements>\n     <version_command>q2galaxy version diversity_lib</version_command>\n     <command detect_errors="exit_code">q2galaxy run diversity_lib beta_phylogenetic_passthrough \'$inputs\'</command>\n     <configfiles>\n-        <inputs name="inputs" data_style="paths"/>\n+        <inputs name="inputs" data_style="staging_path_and_source_path"/>\n     </configfiles>\n     <inputs>\n         <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.">\n@@ -42,18 +42,6 @@\n             <validator type="expression" message="Please verify this parameter.">value != \'__q2galaxy__::literal::None\'</validator>\n         </param>\n         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n-            <conditional name="__q2galaxy__GUI__conditional__threads__">\n-                <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices(\'auto\')" help="[default: 1]  The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = \'auto\', one thread will be created for each identified CPU core on the host.">\n-                    <option value="auto">auto (Str)</option>\n-                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>\n-                </param>\n-                <when value="auto">\n-                    <param name="threads" type="hidden" value="auto"/>\n-                </when>\n-                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">\n-                    <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1]  The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = \'auto\', one thread will be created for each identified CPU core on the host."/>\n-                </when>\n-            </conditional>\n             <param name="variance_adjusted" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="variance_adjusted: Bool" help="[default: No]  Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation."/>\n             <param name="alpha" type="float" min="0" max="1" optional="true" label="alpha: Float % Range(0, 1, inclusive_end=True)" help="[optional]  This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniF'..b'axy__GUI__conditional__threads__">\n-                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>\n-                <param name="threads" value="1"/>\n-            </conditional>\n             <output name="distance_matrix" ftype="qza">\n                 <assert_contents>\n                     <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">\n@@ -95,10 +79,6 @@\n             <param name="table" value="beta_phylogenetic_passthrough.test2.feature-table.qza" ftype="qza"/>\n             <param name="phylogeny" value="beta_phylogenetic_passthrough.test2.phylogeny.qza" ftype="qza"/>\n             <param name="metric" value="weighted_normalized_unifrac"/>\n-            <conditional name="__q2galaxy__GUI__conditional__threads__">\n-                <param name="__q2galaxy__GUI__select__" value="auto"/>\n-                <param name="threads" value="auto"/>\n-            </conditional>\n             <output name="distance_matrix" ftype="qza">\n                 <assert_contents>\n                     <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">\n@@ -111,10 +91,6 @@\n             <param name="table" value="beta_phylogenetic_passthrough.test3.feature-table.qza" ftype="qza"/>\n             <param name="phylogeny" value="beta_phylogenetic_passthrough.test3.phylogeny.qza" ftype="qza"/>\n             <param name="metric" value="weighted_normalized_unifrac"/>\n-            <conditional name="__q2galaxy__GUI__conditional__threads__">\n-                <param name="__q2galaxy__GUI__select__" value="auto"/>\n-                <param name="threads" value="auto"/>\n-            </conditional>\n             <param name="bypass_tips" value="__q2galaxy__::literal::True"/>\n             <output name="distance_matrix" ftype="qza">\n                 <assert_contents>\n@@ -128,10 +104,6 @@\n             <param name="table" value="beta_phylogenetic_passthrough.test4.feature-table.qza" ftype="qza"/>\n             <param name="phylogeny" value="beta_phylogenetic_passthrough.test4.phylogeny.qza" ftype="qza"/>\n             <param name="metric" value="weighted_unifrac"/>\n-            <conditional name="__q2galaxy__GUI__conditional__threads__">\n-                <param name="__q2galaxy__GUI__select__" value="auto"/>\n-                <param name="threads" value="auto"/>\n-            </conditional>\n             <param name="variance_adjusted" value="__q2galaxy__::literal::True"/>\n             <output name="distance_matrix" ftype="qza">\n                 <assert_contents>\n@@ -212,10 +184,6 @@\n  #. Set *"table"* to ``#: feature-table.qza``\n  #. Set *"phylogeny"* to ``#: phylogeny.qza``\n  #. Set *"metric"* to ``weighted_normalized_unifrac``\n- #. Expand the ``additional options`` section\n-\n-    - Leave *"threads"* as its default value of ``1``\n-\n  #. Press the ``Execute`` button.\n \n Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n@@ -236,10 +204,6 @@\n  #. Set *"table"* to ``#: feature-table.qza``\n  #. Set *"phylogeny"* to ``#: phylogeny.qza``\n  #. Set *"metric"* to ``weighted_normalized_unifrac``\n- #. Expand the ``additional options`` section\n-\n-    - Set *"threads"* to ``auto``\n-\n  #. Press the ``Execute`` button.\n \n Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n@@ -263,8 +227,7 @@\n  #. Set *"metric"* to ``weighted_normalized_unifrac``\n  #. Expand the ``additional options`` section\n \n-    #. Set *"threads"* to ``auto``\n-    #. Set *"bypass_tips"* to ``Yes``\n+    - Set *"bypass_tips"* to ``Yes``\n \n  #. Press the ``Execute`` button.\n \n@@ -289,8 +252,7 @@\n  #. Set *"metric"* to ``weighted_unifrac``\n  #. Expand the ``additional options`` section\n \n-    #. Set *"threads"* to ``auto``\n-    #. Set *"variance_adjusted"* to ``Yes``\n+    - Set *"variance_adjusted"* to ``Yes``\n \n  #. Press the ``Execute`` button.\n \n'
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