# HG changeset patch
# User q2d2
# Date 1661803599 0
# Node ID 682de1aeb1ad2cac8fbab5468e7f81f6150029c6

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 682de1aeb1ad qiime2__gneiss__ilr_phylogenetic_differential.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__gneiss__ilr_phylogenetic_differential.xml	Mon Aug 29 20:06:39 2022 +0000
@@ -0,0 +1,77 @@
+<?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 gneiss ilr-phylogenetic-differential" id="qiime2__gneiss__ilr_phylogenetic_differential" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Differentially abundant Phylogenetic Log Ratios.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version gneiss</version_command>
+    <command detect_errors="aggressive">q2galaxy run gneiss ilr_phylogenetic_differential '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="differential" type="data" format="qza" label="differential: FeatureData[Differential]" help="[required]  The differential abundance results in which will be ilr transformed.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Differential]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Differential]']</validator>
+        </param>
+        <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required]  A rooted phylogeny of feature identifiers that defines the partitions of features.  Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.  This assumes that all of the internal nodes in the tree have labels. This tree may contain polytomic nodes (i.e., nodes with more than two children), in which case they will be bifurcated.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="Phylogeny[Rooted]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="ilr_differential" format="qza" label="${tool.name} on ${on_string}: ilr_differential.qza" from_work_dir="ilr_differential.qza"/>
+        <data name="bifurcated_tree" format="qza" label="${tool.name} on ${on_string}: bifurcated_tree.qza" from_work_dir="bifurcated_tree.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: gneiss ilr-phylogenetic-differential
+=============================================
+Differentially abundant Phylogenetic Log Ratios.
+
+
+Outputs:
+--------
+:ilr_differential.qza: Per clade differential abundance results.
+:bifurcated_tree.qza: Bifurcating phylogeny.
+
+|  
+
+Description:
+------------
+Compute an ILR transform of differentials given a rooted phylogeny.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="bibtex">@article{cite1,
+ author = {Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and Vázquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and Lladser, Manuel and Dorrestein, Pieter C and Knight, Rob},
+ journal = {MSystems},
+ number = {1},
+ pages = {e00162--16},
+ publisher = {Am Soc Microbiol},
+ title = {Balance trees reveal microbial niche differentiation},
+ volume = {2},
+ year = {2017}
+}
+</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 682de1aeb1ad test-data/.gitkeep