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Changeset 0:db10f8dee85a (2022-08-29)

Next changeset 1:1ab2573cba43 (2023-01-13)

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

added:
qiime2__diversity__beta_rarefaction.xml
test-data/.gitkeep

diff -r 000000000000 -r db10f8dee85a qiime2__diversity__beta_rarefaction.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__diversity__beta_rarefaction.xml Mon Aug 29 19:30:26 2022 +0000

[

b'@@ -0,0 +1,156 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 diversity beta-rarefaction" id="qiime2__diversity__beta_rarefaction" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">\n+ <description>Beta diversity rarefaction</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <version_command>q2galaxy version diversity</version_command>\n+ <command detect_errors="aggressive">q2galaxy run diversity beta_rarefaction \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table upon which to perform beta diversity rarefaction analyses.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureTable[Frequency]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureTable[Frequency]\']</validator>\n+ </param>\n+ <param name="metric" type="select" label="metric: Str % Choices(\'aitchison\', \'braycurtis\', \'canberra\', \'canberra_adkins\', \'chebyshev\', \'cityblock\', \'correlation\', \'cosine\', \'dice\', \'euclidean\', \'generalized_unifrac\', \'hamming\', \'jaccard\', \'jensenshannon\', \'kulsinski\', \'matching\', \'minkowski\', \'rogerstanimoto\', \'russellrao\', \'seuclidean\', \'sokalmichener\', \'sokalsneath\', \'sqeuclidean\', \'unweighted_unifrac\', \'weighted_normalized_unifrac\', \'weighted_unifrac\', \'yule\')">\n+ <option value="__q2galaxy__::literal::None">Selection required</option>\n+ <option value="aitchison">aitchison</option>\n+ <option value="braycurtis">braycurtis</option>\n+ <option value="canberra">canberra</option>\n+ <option value="canberra_adkins">canberra_adkins</option>\n+ <option value="chebyshev">chebyshev</option>\n+ <option value="cityblock">cityblock</option>\n+ <option value="correlation">correlation</option>\n+ <option value="cosine">cosine</option>\n+ <option value="dice">dice</option>\n+ <option value="euclidean">euclidean</option>\n+ <option value="generalized_unifrac">generalized_unifrac</option>\n+ <option value="hamming">hamming</option>\n+ <option value="jaccard">jaccard</option>\n+ <option value="jensenshannon">jensenshannon</option>\n+ <option value="kulsinski">kulsinski</option>\n+ <option value="matching">matching</option>\n+ <option value="minkowski">minkowski</option>\n+ <option value="rogerstanimoto">rogerstanimoto</option>\n+ <option value="russellrao">russellrao</option>\n+ <option value="seuclidean">seuclidean</option>\n+ <option value="sokalmichener">sokalmichener</option>\n+ <option value="sokalsneath">sokalsneath</option>\n+ <option value="sqeuclidean">sqeuclidean</option>\n+ <option value="unweighted_unifrac">unweighted_unifrac</option>\n+ <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>\n+ <option value="weighted_unifrac">weighted_unifrac</option>\n+ <option value="yule">yule</option>\n+ <validator type="expression" message="Please verify this parameter.">value != \'__q2galaxy__::literal::None\'</validator>\n+ </param>\n+ <param name="clustering_method" type="select" label="clustering_method: Str % Choices(\'nj\', \'upgma\')" '..b'ing the diversity metric."/>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <param name="phylogeny" type="data" format="qza" optional="true" label="phylogeny: Phylogeny[Rooted]" help="[optional] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics]">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="Phylogeny[Rooted]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'Phylogeny[Rooted]\']</validator>\n+ </param>\n+ <param name="iterations" type="integer" min="2" value="10" label="iterations: Int % Range(2, None)" help="[default: 10] Number of times to rarefy the feature table at a given sampling depth."/>\n+ <param name="correlation_method" type="select" label="correlation_method: Str % Choices(\'pearson\', \'spearman\')" display="radio">\n+ <option value="pearson">pearson</option>\n+ <option value="spearman" selected="true">spearman</option>\n+ </param>\n+ <param name="color_scheme" type="select" label="color_scheme: Str % Choices(\'BrBG\', \'BrBG_r\', \'PRGn\', \'PRGn_r\', \'PiYG\', \'PiYG_r\', \'PuOr\', \'PuOr_r\', \'RdBu\', \'RdBu_r\', \'RdGy\', \'RdGy_r\', \'RdYlBu\', \'RdYlBu_r\', \'RdYlGn\', \'RdYlGn_r\')">\n+ <option value="BrBG" selected="true">BrBG</option>\n+ <option value="BrBG_r">BrBG_r</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="PRGn_r">PRGn_r</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PiYG_r">PiYG_r</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuOr_r">PuOr_r</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdBu_r">RdBu_r</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdGy_r">RdGy_r</option>\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="RdYlBu_r">RdYlBu_r</option>\n+ <option value="RdYlGn">RdYlGn</option>\n+ <option value="RdYlGn_r">RdYlGn_r</option>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: diversity beta-rarefaction\n+===================================\n+Beta diversity rarefaction\n+\n+\n+Outputs:\n+--------\n+:visualization.qzv: <no description>\n+\n+| \n+\n+Description:\n+------------\n+Repeatedly rarefy a feature table to compare beta diversity results within a given rarefaction depth.\n+\n+For a given beta diversity metric, this visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered by UPGMA or neighbor joining with support calculation, and a heatmap showing the correlation between rarefaction trials of that beta diversity metric.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="bibtex">@article{cite1,\n+ author = {Mantel, Nathan},\n+ journal = {Cancer research},\n+ number = {2 Part 1},\n+ pages = {209--220},\n+ publisher = {AACR},\n+ title = {The detection of disease clustering and a generalized regression approach},\n+ volume = {27},\n+ year = {1967}\n+}\n+</citation>\n+ <citation type="doi">https://doi.org/10.1098/rspl.1895.0041</citation>\n+ <citation type="doi">https://doi.org/10.2307/1422689</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'