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changeset 0:c841290b1a15 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 19:35:49 +0000
parents
children 4b8cdacb02f5
files qiime2__diversity__core_metrics.xml test-data/.gitkeep
diffstat 1 files changed, 106 insertions(+), 0 deletions(-) [+]
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+++ b/qiime2__diversity__core_metrics.xml	Mon Aug 29 19:35:49 2022 +0000
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+<?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 core-metrics" id="qiime2__diversity__core_metrics" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Core diversity metrics (non-phylogenetic)</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 core_metrics '$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 diversity metrics 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="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required]  The total frequency that each sample should be rarefied to prior to computing diversity metrics."/>
+        <repeat name="metadata" min="1" help="[required]  The sample metadata to use in the emperor plots." title="metadata: Metadata">
+            <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                <param name="type" type="select" label="metadata: Metadata">
+                    <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"/>
+                </when>
+                <when value="qza">
+                    <param name="source" type="data" format="qza" label="Metadata Source"/>
+                </when>
+            </conditional>
+        </repeat>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="with_replacement" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="with_replacement: Bool" help="[default: No]  Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement."/>
+            <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]  [beta methods only] - 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]  [beta methods only] - 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="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/>
+        <data name="observed_features_vector" format="qza" label="${tool.name} on ${on_string}: observed_features_vector.qza" from_work_dir="observed_features_vector.qza"/>
+        <data name="shannon_vector" format="qza" label="${tool.name} on ${on_string}: shannon_vector.qza" from_work_dir="shannon_vector.qza"/>
+        <data name="evenness_vector" format="qza" label="${tool.name} on ${on_string}: evenness_vector.qza" from_work_dir="evenness_vector.qza"/>
+        <data name="jaccard_distance_matrix" format="qza" label="${tool.name} on ${on_string}: jaccard_distance_matrix.qza" from_work_dir="jaccard_distance_matrix.qza"/>
+        <data name="bray_curtis_distance_matrix" format="qza" label="${tool.name} on ${on_string}: bray_curtis_distance_matrix.qza" from_work_dir="bray_curtis_distance_matrix.qza"/>
+        <data name="jaccard_pcoa_results" format="qza" label="${tool.name} on ${on_string}: jaccard_pcoa_results.qza" from_work_dir="jaccard_pcoa_results.qza"/>
+        <data name="bray_curtis_pcoa_results" format="qza" label="${tool.name} on ${on_string}: bray_curtis_pcoa_results.qza" from_work_dir="bray_curtis_pcoa_results.qza"/>
+        <data name="jaccard_emperor" format="qzv" label="${tool.name} on ${on_string}: jaccard_emperor.qzv" from_work_dir="jaccard_emperor.qzv"/>
+        <data name="bray_curtis_emperor" format="qzv" label="${tool.name} on ${on_string}: bray_curtis_emperor.qzv" from_work_dir="bray_curtis_emperor.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: diversity core-metrics
+===============================
+Core diversity metrics (non-phylogenetic)
+
+
+Outputs:
+--------
+:rarefied_table.qza: The resulting rarefied feature table.
+:observed_features_vector.qza: Vector of Observed Features values by sample.
+:shannon_vector.qza: Vector of Shannon diversity values by sample.
+:evenness_vector.qza: Vector of Pielou's evenness values by sample.
+:jaccard_distance_matrix.qza: Matrix of Jaccard distances between pairs of samples.
+:bray_curtis_distance_matrix.qza: Matrix of Bray-Curtis distances between pairs of samples.
+:jaccard_pcoa_results.qza: PCoA matrix computed from Jaccard distances between samples.
+:bray_curtis_pcoa_results.qza: PCoA matrix computed from Bray-Curtis distances between samples.
+:jaccard_emperor.qzv: Emperor plot of the PCoA matrix computed from Jaccard.
+:bray_curtis_emperor.qzv: Emperor plot of the PCoA matrix computed from Bray-Curtis.
+
+|  
+
+Description:
+------------
+Applies a collection of diversity metrics (non-phylogenetic) to a feature table.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>