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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd
author ufz
date Wed, 16 Apr 2025 09:42:52 +0000
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-1:000000000000 0:0e7bd9c4dd43
1 <tool id="phabox_tree" name="PhaBOX tree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
2 <description>Build phylogenetic trees based on marker genes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">phabox</xref>
8 </xrefs>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">phabox</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13 phabox2 --task tree
14 @GENERAL@
15 @TREE@
16 ]]></command>
17 <inputs>
18 <expand macro="general"/>
19 <expand macro="tree"/>
20 </inputs>
21 <outputs>
22 <collection name="marker_genes" format="fasta" type="list">
23 <discover_datasets pattern="found_marker_(?P&lt;designation&gt;.+)_combined_db.fa" directory="output/final_prediction/tree_supplementary"/>
24 </collection>
25 </outputs>
26 <tests>
27 <test expect_num_outputs="1">
28 <param name="dbdir" value="phaboxdb"/>
29 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
30 <output_collection name="marker_genes" count="2">
31 <element name="portal">
32 <assert_contents>
33 <has_text text=">" n="4281"/>
34 </assert_contents>
35 </element>
36 <element name="terl">
37 <assert_contents>
38 <has_text text=">" n="4672"/>
39 </assert_contents>
40 </element>
41 </output_collection>
42 </test>
43 </tests>
44 <help><![CDATA[
45 Get sequences of specific marker genes that can be used for phylogentic tree construction.
46
47 @COMMON_INPUT_DOC@
48
49 ]]></help>
50 <expand macro="citations"/>
51 </tool>