# HG changeset patch
# User q2d2
# Date 1673650734 0
# Node ID 43e5dd36de74b5b04708da2aa1e7b232c1ba6301
# Parent fd05e62ba9f9b0a537eb45e281fb9b2fc1a6bc34
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 69da7976573cc07a363ac66bdacc9269d7cd3732
diff -r fd05e62ba9f9 -r 43e5dd36de74 qiime2__phylogeny__align_to_tree_mafft_fasttree.xml
--- a/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml Mon Aug 29 20:16:51 2022 +0000
+++ b/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml Fri Jan 13 22:58:54 2023 +0000
@@ -1,22 +1,22 @@
<?xml version='1.0' encoding='utf-8'?>
<!--
-Copyright (c) 2022, QIIME 2 development team.
+Copyright (c) 2023, 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)
+ q2galaxy (version: 2022.11.1)
for:
- qiime2 (version: 2022.8.1)
+ qiime2 (version: 2022.11.1)
-->
-<tool name="qiime2 phylogeny align-to-tree-mafft-fasttree" id="qiime2__phylogeny__align_to_tree_mafft_fasttree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 phylogeny align-to-tree-mafft-fasttree" id="qiime2__phylogeny__align_to_tree_mafft_fasttree" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
<description>Build a phylogenetic tree using fasttree and mafft alignment</description>
<requirements>
- <container type="docker">quay.io/qiime2/core:2022.8</container>
+ <container type="docker">quay.io/qiime2/core:2022.11</container>
</requirements>
<version_command>q2galaxy version phylogeny</version_command>
- <command detect_errors="aggressive">q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs'</command>
+ <command detect_errors="exit_code">q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs'</command>
<configfiles>
<inputs name="inputs" data_style="paths"/>
</configfiles>
@@ -51,7 +51,39 @@
<data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
<data name="rooted_tree" format="qza" label="${tool.name} on ${on_string}: rooted_tree.qza" from_work_dir="rooted_tree.qza"/>
</outputs>
- <tests/>
+ <tests>
+ <test>
+ <param name="sequences" value="align_to_tree_mafft_fasttree.test0.rep-seqs.qza" ftype="qza"/>
+ <output name="alignment" ftype="qza">
+ <assert_contents>
+ <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+ <has_line_matching expression="type: FeatureData\[AlignedSequence\]"/>
+ </has_archive_member>
+ </assert_contents>
+ </output>
+ <output name="masked_alignment" ftype="qza">
+ <assert_contents>
+ <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+ <has_line_matching expression="type: FeatureData\[AlignedSequence\]"/>
+ </has_archive_member>
+ </assert_contents>
+ </output>
+ <output name="tree" ftype="qza">
+ <assert_contents>
+ <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+ <has_line_matching expression="type: Phylogeny\[Unrooted\]"/>
+ </has_archive_member>
+ </assert_contents>
+ </output>
+ <output name="rooted_tree" ftype="qza">
+ <assert_contents>
+ <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+ <has_line_matching expression="type: Phylogeny\[Rooted\]"/>
+ </has_archive_member>
+ </assert_contents>
+ </output>
+ </test>
+ </tests>
<help>
QIIME 2: phylogeny align-to-tree-mafft-fasttree
===============================================
@@ -71,6 +103,33 @@
------------
This pipeline will start by creating a sequence alignment using MAFFT, after which any alignment columns that are phylogenetically uninformative or ambiguously aligned will be removed (masked). The resulting masked alignment will be used to infer a phylogenetic tree and then subsequently rooted at its midpoint. Output files from each step of the pipeline will be saved. This includes both the unmasked and masked MAFFT alignment from q2-alignment methods, and both the rooted and unrooted phylogenies from q2-phylogeny methods.
+Examples:
+---------
+
+align_to_tree_mafft_fasttree
+****************************
+Using the ``qiime2 phylogeny align-to-tree-mafft-fasttree`` tool:
+ #. Set *"sequences"* to ``#: rep-seqs.qza``
+ #. Press the ``Execute`` button.
+
+Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+ :align: left
+ :header-rows: 1
+
+ * - History Name
+ - *"Name"* to set (be sure to press ``Save``)
+ * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : alignment.qza``
+ - ``aligned-rep-seqs.qza``
+ * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : masked_alignment.qza``
+ - ``masked-aligned-rep-seqs.qza``
+ * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : tree.qza``
+ - ``unrooted-tree.qza``
+ * - ``#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : rooted_tree.qza``
+ - ``rooted-tree.qza``
+
|
diff -r fd05e62ba9f9 -r 43e5dd36de74 test-data/.gitkeep
diff -r fd05e62ba9f9 -r 43e5dd36de74 test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza
Binary file test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza has changed