--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pharokka.xml	Fri Mar 13 12:17:54 2026 +0000
@@ -0,0 +1,166 @@
+<tool id="pharokka" name="pharokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Rapid standardised annotation tool for bacteriophage genomes and metagenomes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        
+    </macros>
+    <expand macro="biotools" />
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code">
+        <![CDATA[
+
+        ##run tool
+        #if str( $terminase.terminase_selector ) == 'no_terminase':
+        pharokka.py 
+        -i '$fasta'
+        -o pharokka_output
+        -d '$db_cached.fields.path'
+        -t \${GALAXY_SLOTS:-8} 
+        $gene_predictor
+        $meta
+        -e '$evalue' 
+        #else:
+        pharokka.py 
+        -i '$fasta' 
+        -o pharokka_output 
+        -d '$db_cached.fields.path' 
+        -t \${GALAXY_SLOTS:-8} 
+        $gene_predictor 
+        $meta 
+        -e '$evalue' 
+        --terminase 
+        --terminase_strand '$terminase.terminase_strand' 
+        --terminase_start '$terminase.terminase_start' 
+        #end if
+        
+        ## create output
+        #if $zip_output == 'true':
+            && zip -r out.zip pharokka_output
+        #end if
+        ]]>
+    </command>
+    <inputs>
+        <!-- the genome -->
+        <param type="data" name="fasta" format="fasta" help="Please upload a genome file of a bacteriophage in fasta format." label="Bacteriophage genome" />
+        <param name="db_cached" type="select" label="Using built-in pharokka DB" help="Using built-in pharokka DB">
+            <options from_data_table="pharokka_db_versioned">
+            </options>
+            <validator type="no_options" message="A built-in pharokka DB is not available. Please ask the galaxy admins to install one on the server." />
+        </param>
+        <param name="gene_predictor" type="select" label="User specified gene predictor">
+            <option value="-g phanotate">
+                Phanotate
+            </option>
+            <option value="-g prodigal">
+                Prodigal
+            </option>
+        </param>
+        <param name="meta" type="boolean" checked="false" truevalue="--meta" falsevalue="" label="Meta mode for metavirome input samples" />
+        <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." />
+        <!-- optional arguments -->
+        <conditional name="terminase">
+            <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.">
+                <option value="no_terminase">
+                    Do not run 'terminase large subunit' re-orientation mode.
+                </option>
+                <option value="run_terminase">
+                    Runs 'terminase large subunit' re-orientation mode.
+                </option>
+            </param>
+            <when value="no_terminase">
+            </when>
+            <when value="run_terminase">
+                <param name="terminase_strand" type="select" label="Strand of terminase large subunit.">
+                    <option value="pos">
+                        Positive
+                    </option>
+                    <option value="neg">
+                        Negative
+                    </option>
+                </param>
+                <param name="terminase_start" type="integer" value="1" label="Start coordinate of the terminase large subunit." />
+            </when>
+        </conditional>
+        <!-- optional outputs -->
+        <param name="zip_output" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Create a Zip archive of the complete output for further investigation." />
+    </inputs>
+    <outputs>
+        <data name="pharokka_gbk" format="genbank" from_work_dir="pharokka_output/pharokka.gbk" label="${tool.name} on ${on_string}: Genbank" />
+        <data name="pharokka_gff" format="gff" from_work_dir="pharokka_output/pharokka.gff" label="${tool.name} on ${on_string}: GFF" />
+        <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" >
+            <filter>zip_output</filter>
+        </data>
+
+    </outputs>
+    <tests>
+        <!-- test input from DB - no zip -->
+        <test expect_num_outputs="2">
+            <param name="db_cached" value="pharokka_db" />
+            <param name="fasta" value="SAOMS1.fasta" />
+            <param name="zip_output" value="false" />
+            <!-- check file size and text since output is non-deterministic -->
+            <output name="pharokka_gbk">
+                <assert_contents>
+                    <has_size value="353875" delta="10" />
+                    <has_text text="VERSION     MW460250_1" />
+                </assert_contents>
+            </output>
+            <output name="pharokka_gff">
+                <assert_contents>
+                    <has_size value="191497" delta="10" />
+                    <has_text text="##sequence-region MW460250_1 1 140135" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test input from DB -->
+        <test expect_num_outputs="3">
+            <param name="db_cached" value="pharokka_db" />
+            <param name="fasta" value="SAOMS1.fasta" />
+            <param name="zip_output" value="true" />
+            <!-- check file size and text since output is non-deterministic -->
+            <output name="pharokka_gbk">
+                <assert_contents>
+                    <has_size value="353875" delta="10" />
+                    <has_text text="VERSION     MW460250_1" />
+                </assert_contents>
+            </output>
+            <output name="pharokka_gff">
+                <assert_contents>
+                    <has_size value="191497" delta="10" />
+                    <has_text text="##sequence-region MW460250_1 1 140135" />
+                </assert_contents>
+            </output>
+            <!-- check created zip -->
+            <output name="archive_output">
+                <assert_contents>
+                    <has_archive_member path=".*\/pharokka\.gff" />
+                    <has_archive_member path=".*\/pharokka\.gbk" />
+                    <has_archive_member path=".*\/pharokka.*\.log" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+        Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.
+        Pharokka identifies predicted coding sequences (CDS), transfer RNAs (tRNAs),
+        transfer-messenger RNAs (tmRNAs) and clustered regularly interspaced short 
+        palindromic repeats (CRISPRs), providing functional annotation for CDS using the PHROGs database. 
+        
+        Pharokka requires assembled DNA sequences in FASTA format.
+        For phage isolates, this usually consists of one complete contig, 
+        but Pharokka can also annotate incomplete assemblies or metavirome samples with multiple 
+        contigs in the multiFASTA format. 
+        Furthermore, metagenomically assembled phage genomes and genomic contigs, 
+        derived using programs such as Virstorter2, Hecatomb and Cenote-taker 2, 
+        are also suitable to be annotated using Pharokka using meta mode.
+
+        If you are looking for rapid standardised annotation of bacterial genomes, please use bakta.
+        ]]>
+    </help>
+    <expand macro="citations" />
+    <expand macro="creator" />
+</tool>