Mercurial > repos > q2d2 > qiime2phylogenyraxml

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__phylogeny__raxml.xml	Mon Aug 29 20:15:31 2022 +0000
@@ -0,0 +1,75 @@
+<?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 phylogeny raxml" id="qiime2__phylogeny__raxml" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Construct a phylogenetic tree with RAxML.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version phylogeny</version_command>
+    <command detect_errors="aggressive">q2galaxy run phylogeny raxml '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  Aligned sequences to be used for phylogenetic reconstruction.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional]  Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>
+            <param name="n_searches" type="integer" min="1" value="1" label="n_searches: Int % Range(1, None)" help="[default: 1]  The number of independent maximum likelihood searches to perform. The single best scoring tree is returned."/>
+            <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML."/>
+            <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio">
+                <option value="Standard" selected="true">Standard</option>
+                <option value="SSE3">SSE3</option>
+                <option value="AVX2">AVX2</option>
+            </param>
+            <param name="substitution_model" type="select" label="substitution_model: Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI')" display="radio">
+                <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
+                <option value="GTRGAMMAI">GTRGAMMAI</option>
+                <option value="GTRCAT">GTRCAT</option>
+                <option value="GTRCATI">GTRCATI</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: phylogeny raxml
+========================
+Construct a phylogenetic tree with RAxML.
+
+
+Outputs:
+--------
+:tree.qza: The resulting phylogenetic tree.
+
+|
+
+Description:
+------------
+Construct a phylogenetic tree with RAxML. See: https://sco.h-its.org/exelixis/web/software/raxml/
+
+
+|
+
+</help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu033</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>