# HG changeset patch
# User q2d2
# Date 1661803495 0
# Node ID 6f99999790ebb16dd5e5d2753ddcecab1960dcec

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

diff -r 000000000000 -r 6f99999790eb qiime2__gneiss__assign_ids.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__gneiss__assign_ids.xml	Mon Aug 29 20:04:55 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 assign-ids" id="qiime2__gneiss__assign_ids" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</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 assign_ids '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="input_table" type="data" format="qza" label="input_table: FeatureTable[Frequency]" help="[required]  The input table of counts.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
+        </param>
+        <param name="input_tree" type="data" format="qza" label="input_tree: Phylogeny[Rooted]" help="[required]  The input tree with potential missing ids.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="Phylogeny[Rooted]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_table" format="qza" label="${tool.name} on ${on_string}: output_table.qza" from_work_dir="output_table.qza"/>
+        <data name="output_tree" format="qza" label="${tool.name} on ${on_string}: output_tree.qza" from_work_dir="output_tree.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: gneiss assign-ids
+==========================
+Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
+
+
+Outputs:
+--------
+:output_table.qza: A table with features matching the tree tips.
+:output_tree.qza: A tree with uniquely identifying ids.
+
+|  
+
+Description:
+------------
+Assigns UUIDs to uniquely identify internal nodes in the tree.  Also corrects for polytomies to create strictly bifurcating trees and aligns the table columns with the tree tip names
+
+
+|  
+
+</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 6f99999790eb test-data/.gitkeep