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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 09:42:24 +0000
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1 <tool id="phabox_cherry" name="PhaBOX cherry" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
2 <description>Host prediction</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 @CRISPR_PRE@
14 phabox2 --task cherry
15 @GENERAL@
16 @NETWORK@
17 @CRISPR@
18 ]]></command>
19 <inputs>
20 <expand macro="general"/>
21 <expand macro="network"/>
22 <expand macro="crispr"/>
23 </inputs>
24 <outputs>
25 <data name="out" format="tabular" from_work_dir="output/final_prediction/cherry_prediction.tsv"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="dbdir" value="phaboxdb"/>
30 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
31 <output name="out">
32 <assert_contents>
33 <has_line line="Accession&#9;Length&#9;Host&#9;CHERRYScore&#9;Method&#9;Host_NCBI_lineage&#9;Host_GTDB_lineage"/>
34 <has_n_lines n="391"/>
35 <has_n_columns n="7"/>
36 </assert_contents>
37 </output>
38 </test>
39 </tests>
40 <help><![CDATA[
41 Predict hosts for viruses.
42
43
44 @COMMON_INPUT_DOC@
45
46 **Output**
47
48 @COMMON_OUTPUT_DOC@
49 @CHERRY_OUTPUT_DOC@
50 ]]></help>
51 <expand macro="citations">
52 <citation type="doi">10.1093/bib/bbac182</citation>
53 </expand>
54 </tool>