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