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planemo upload commit 897d2d95060ea3cb3f904d53d9d7e0f26644b005
author estrain
date Fri, 13 Mar 2026 12:17:54 +0000
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1 <tool id="pharokka" name="pharokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Rapid standardised annotation tool for bacteriophage genomes and metagenomes
4 </description>
5 <macros>
6 <import>macros.xml</import>
7
8 </macros>
9 <expand macro="biotools" />
10 <expand macro="requirements" />
11 <expand macro="version" />
12 <command detect_errors="exit_code">
13 <![CDATA[
14
15 ##run tool
16 #if str( $terminase.terminase_selector ) == 'no_terminase':
17 pharokka.py
18 -i '$fasta'
19 -o pharokka_output
20 -d '$db_cached.fields.path'
21 -t \${GALAXY_SLOTS:-8}
22 $gene_predictor
23 $meta
24 -e '$evalue'
25 #else:
26 pharokka.py
27 -i '$fasta'
28 -o pharokka_output
29 -d '$db_cached.fields.path'
30 -t \${GALAXY_SLOTS:-8}
31 $gene_predictor
32 $meta
33 -e '$evalue'
34 --terminase
35 --terminase_strand '$terminase.terminase_strand'
36 --terminase_start '$terminase.terminase_start'
37 #end if
38
39 ## create output
40 #if $zip_output == 'true':
41 && zip -r out.zip pharokka_output
42 #end if
43 ]]>
44 </command>
45 <inputs>
46 <!-- the genome -->
47 <param type="data" name="fasta" format="fasta" help="Please upload a genome file of a bacteriophage in fasta format." label="Bacteriophage genome" />
48 <param name="db_cached" type="select" label="Using built-in pharokka DB" help="Using built-in pharokka DB">
49 <options from_data_table="pharokka_db_versioned">
50 </options>
51 <validator type="no_options" message="A built-in pharokka DB is not available. Please ask the galaxy admins to install one on the server." />
52 </param>
53 <param name="gene_predictor" type="select" label="User specified gene predictor">
54 <option value="-g phanotate">
55 Phanotate
56 </option>
57 <option value="-g prodigal">
58 Prodigal
59 </option>
60 </param>
61 <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="Meta mode for metavirome input samples" />
62 <param name="evalue" type="float" value="1E-5" min="1E-20" max="10" label="E-value threshold for mmseqs2 PHROGs database search. Defaults to 1E-05." />
63 <!-- optional arguments -->
64 <conditional name="terminase">
65 <param name="terminase_selector" type="select" label="Runs - terminase large subunit - re-orientation mode. Single genome input only and requires --terminase_strand and --terminase_start to be specified.">
66 <option value="no_terminase">
67 Do not run 'terminase large subunit' re-orientation mode.
68 </option>
69 <option value="run_terminase">
70 Runs 'terminase large subunit' re-orientation mode.
71 </option>
72 </param>
73 <when value="no_terminase">
74 </when>
75 <when value="run_terminase">
76 <param name="terminase_strand" type="select" label="Strand of terminase large subunit.">
77 <option value="pos">
78 Positive
79 </option>
80 <option value="neg">
81 Negative
82 </option>
83 </param>
84 <param name="terminase_start" type="integer" value="1" label="Start coordinate of the terminase large subunit." />
85 </when>
86 </conditional>
87 <!-- optional outputs -->
88 <param name="zip_output" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Create a Zip archive of the complete output for further investigation." />
89 </inputs>
90 <outputs>
91 <data name="pharokka_gbk" format="genbank" from_work_dir="pharokka_output/pharokka.gbk" label="${tool.name} on ${on_string}: Genbank" />
92 <data name="pharokka_gff" format="gff" from_work_dir="pharokka_output/pharokka.gff" label="${tool.name} on ${on_string}: GFF" />
93 <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" >
94 <filter>zip_output</filter>
95 </data>
96
97 </outputs>
98 <tests>
99 <!-- test input from DB - no zip -->
100 <test expect_num_outputs="2">
101 <param name="db_cached" value="pharokka_db" />
102 <param name="fasta" value="SAOMS1.fasta" />
103 <param name="zip_output" value="false" />
104 <!-- check file size and text since output is non-deterministic -->
105 <output name="pharokka_gbk">
106 <assert_contents>
107 <has_size value="353875" delta="10" />
108 <has_text text="VERSION MW460250_1" />
109 </assert_contents>
110 </output>
111 <output name="pharokka_gff">
112 <assert_contents>
113 <has_size value="191497" delta="10" />
114 <has_text text="##sequence-region MW460250_1 1 140135" />
115 </assert_contents>
116 </output>
117 </test>
118 <!-- test input from DB -->
119 <test expect_num_outputs="3">
120 <param name="db_cached" value="pharokka_db" />
121 <param name="fasta" value="SAOMS1.fasta" />
122 <param name="zip_output" value="true" />
123 <!-- check file size and text since output is non-deterministic -->
124 <output name="pharokka_gbk">
125 <assert_contents>
126 <has_size value="353875" delta="10" />
127 <has_text text="VERSION MW460250_1" />
128 </assert_contents>
129 </output>
130 <output name="pharokka_gff">
131 <assert_contents>
132 <has_size value="191497" delta="10" />
133 <has_text text="##sequence-region MW460250_1 1 140135" />
134 </assert_contents>
135 </output>
136 <!-- check created zip -->
137 <output name="archive_output">
138 <assert_contents>
139 <has_archive_member path=".*\/pharokka\.gff" />
140 <has_archive_member path=".*\/pharokka\.gbk" />
141 <has_archive_member path=".*\/pharokka.*\.log" />
142 </assert_contents>
143 </output>
144 </test>
145 </tests>
146 <help>
147 <![CDATA[
148 Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
149 Pharokka identifies predicted coding sequences (CDS), transfer RNAs (tRNAs),
150 transfer-messenger RNAs (tmRNAs) and clustered regularly interspaced short
151 palindromic repeats (CRISPRs), providing functional annotation for CDS using the PHROGs database.
152
153 Pharokka requires assembled DNA sequences in FASTA format.
154 For phage isolates, this usually consists of one complete contig,
155 but Pharokka can also annotate incomplete assemblies or metavirome samples with multiple
156 contigs in the multiFASTA format.
157 Furthermore, metagenomically assembled phage genomes and genomic contigs,
158 derived using programs such as Virstorter2, Hecatomb and Cenote-taker 2,
159 are also suitable to be annotated using Pharokka using meta mode.
160
161 If you are looking for rapid standardised annotation of bacterial genomes, please use bakta.
162 ]]>
163 </help>
164 <expand macro="citations" />
165 <expand macro="creator" />
166 </tool>