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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 09:42:31 +0000
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1 <tool id="phabox_phavip" name="PhaBOX phavip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT">
2 <description>Protein annotation</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 phavip
14 @GENERAL@
15 ]]></command>
16 <inputs>
17 <expand macro="general"/>
18 <param name="supp_outputs" type="select" optional="true" label="Supplementary outputs">
19 <option value="gene_annotation">Gene annotation</option>
20 </param>
21 </inputs>
22 <outputs>
23 <data name="out" format="tabular" from_work_dir="output/final_prediction/phavip_prediction.tsv"/>
24 <data name="phavip_annotation" format="tabular" from_work_dir="output/final_prediction/phavip_supplementary/gene_annotation.tsv" label="${tool.name} on ${on_string}: Gene annotation">
25 <filter>supp_outputs and "gene_annotation" in supp_outputs</filter>
26 </data>
27 </outputs>
28 <tests>
29 <test expect_num_outputs="1">
30 <param name="dbdir" value="phaboxdb"/>
31 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
32 <output name="out">
33 <assert_contents>
34 <has_line line="Accession&#9;Length&#9;Protein_num&#9;Annotated_num&#9;Annotation_rate"/>
35 <has_n_lines n="391"/>
36 <has_n_columns n="5"/>
37 </assert_contents>
38 </output>
39 </test>
40 <test expect_num_outputs="2">
41 <param name="dbdir" value="phaboxdb"/>
42 <param name="contigs" value="example_contigs.fa" location="https://github.com/KennthShang/PhaBOX/releases/download/v2/example_contigs.fa"/>
43 <param name="supp_outputs" value="gene_annotation"/>
44 <output name="out">
45 <assert_contents>
46 <has_line line="Accession&#9;Length&#9;Protein_num&#9;Annotated_num&#9;Annotation_rate"/>
47 <has_n_lines n="391"/>
48 <has_n_columns n="5"/>
49 </assert_contents>
50 </output>
51 <output name="phavip_annotation">
52 <assert_contents>
53 <has_line line="Genome&#9;ORF&#9;Start&#9;End&#9;Strand&#9;GC&#9;Annotation&#9;pident&#9;coverage"/>
54 <has_n_lines n="8995"/>
55 <has_n_columns n="9"/>
56 </assert_contents>
57 </output>
58 </test>
59 </tests>
60 <help><![CDATA[
61
62 Please note that running task end_to_end, phamer, phagcn, phatyp, and cherry, will automatically run phavip.
63 The output files are the same but the supplementary files will be dumped into the corresponding task.
64
65
66 @COMMON_INPUT_DOC@
67
68 **Output**
69
70 @COMMON_OUTPUT_DOC@
71 - Protein_num: total number of predicted proteins.
72 - Annotated_num: number of proteins that have significant alignments.
73 - Annotation_rate: percentage of proteins that have annotations.
74
75 In addition the gene annotation itself can be produced:
76
77 - Genome: the accession or the name of the input contigs.
78 - ORF: the ID of the translated protein.
79 - Start: start position on the genome.
80 - End: end position on the genome.
81 - Strand: forward (1) or backward(-1).
82 - GC: GC content.
83 - Annotation: the annotation of the proteins.
84
85 Please note that there are two kinds of hypothetical protein:
86
87 - hypothetical protein (no hit): a protein has no alignment results to the reference database.
88 - hypothetical protein (no hit): a protein has alignment results but the annotation is "hypothetical protein"
89
90
91 ]]></help>
92 <expand macro="citations"/>
93 </tool>