amrfinderplus.xml

<tool id="amrfinderplus" name="AMRFinderPlus" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        NCBI Antimicrobial Resistance Gene Finder 
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        amrfinder
        #*======================================
                    CPU option
        ======================================*#
        --threads "\${GALAXY_SLOTS:-1}"
        #*======================================
                    DATABASE
        ======================================*#
        --database '$input_option.amrfinder_db_select.fields.path'
        #*======================================
                    INPUT TYPE
        ======================================*#
        #if $input_option.input_mode.input_select == 'nucleotide'
            --nucleotide '$input_option.input_mode.nucleotide_input'
            #if $input_option.input_mode.nucleotide_flank5_size > 0
                --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
                --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
            #end if
            --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
        #elif $input_option.input_mode.input_select == 'protein'
            --protein '$input_option.input_mode.protein_input'
            #if $input_option.input_mode.gff_annotation
                --gff '$input_option.input_mode.gff_annotation'
            #end if
            #if $input_option.input_mode.annotation_format
                --annotation_format $input_option.input_mode.annotation_format
            #end if
            --protein_output 'amrfinderplus_protein_output.fasta'
        #else
            --nucleotide '$input_option.input_mode.nucleotide_input'
            #if $input_option.input_mode.nucleotide_flank5_size and $input_option.input_mode.nucleotide_flank5_size > 0
                --nucleotide_flank5_size $input_option.input_mode.nucleotide_flank5_size
                --nucleotide_flank5_output 'amrfinderplus_flanking_sequence_output.fasta'
            #end if
            --protein '$input_option.input_mode.protein_input'
            --gff '$input_option.input_mode.gff_annotation'
            --annotation_format $input_option.input_mode.annotation_format
            --nucleotide_output 'amrfinderplus_nucleotide_output.fasta'
            --protein_output 'amrfinderplus_protein_output.fasta'
        #end if
        #*======================================
                    ORGANISM PART
        ======================================*#
        #if $organism_options.organism_conditionnal.organism_select
            --organism '$organism_options.organism_conditionnal.organism'
            #if $organism_options.organism_conditionnal.mutation_all
                $organism_options.organism_conditionnal.mutation_all 'mutation_all_report.tsv'
            #end if
            #if $options.plus
                $organism_options.organism_conditionnal.report_common 
            #end if
        #end if
        #*======================================
                        OPTIONS
        ======================================*#
        --ident_min '$options.ident_min'
        --coverage_min '$options.coverage_min'
        #if '$options.translation_table'
            --translation_table '$options.translation_table'
        #end if
        #if '$options.name'
            --name '$options.name'
        #end if
        $options.plus
        $options.report_all_equal
        $options.print_node
        --output 'amrfinderplus_report.tsv'

        ]]></command>
    <inputs>
        <!-- DB and file INPUT -->
        <section name="input_option" title="Input/Output options" expanded="true">
            <param name="amrfinder_db_select" type="select" label="The amrfinderplus database">
                <options from_data_table="amrfinderplus_versioned_database">
                    <filter type="static_value" value="3.12" column="db_version"/>
                    <filter type="unique_value" column="name"/>
                    <validator message="No amrfinderplus database is available" type="no_options"/>
                </options>
            </param>
            <conditional name="input_mode">
                <param name="input_select" type="select" label="Choose input type" help="Choose the type of files (nucleotide and/or protein to be analyzed)">
                    <option value="nucleotide">Nucleotide</option>
                    <option value="protein">Protein</option>
                    <option value="nucl_prot">Nucleotide and Protein</option>
                </param>
                <when value="nucleotide">
                    <expand macro="nucl_input" option="false"/>
                    <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/> 
                </when>
                <when value="protein">
                    <expand macro="prot_input" option="false"/>
                    <expand macro="annotation_type" option="true"/>   
                </when>
                <when value="nucl_prot">
                    <expand macro="nucl_input" option="false"/>
                    <expand macro="prot_input" option="false"/>
                    <expand macro="annotation_type" option="false"/>
                    <param argument="--nucleotide_flank5_size" optional="true" type="integer" min="0" value="0" label="5' flanking sequence size added with sequence match"/> 
                </when>
            </conditional>
        </section>
        <!-- ORGANISM OPTIONS -->
        <section name="organism_options" title="Organism options">
            <conditional name="organism_conditionnal">
                <param name="organism_select" type="select" label="Add organism specifications">
                    <option value="" selected="true">No specifications</option>
                    <option value="add_organism">Add organism specifications</option>
                </param>
                <when value="add_organism">
                    <param argument="--organism" type="select" optional="false" label="Taxonomy group point mutation" help="Choose a taxonomic group to point mutation screening">
                        <option value="Acinetobacter_baumannii">Acinetobacter_baumannii</option>
                        <option value="Burkholderia_cepacia">Burkholderia_cepacia</option>
                        <option value="Burkholderia_pseudomallei">Burkholderia_pseudomallei</option>
                        <option value="Campylobacter">Campylobacter</option>
                        <option value="Citrobacter_freundii">Citrobacter_freundii</option>
                        <option value="Clostridioides_difficile">Clostridioides_difficile</option>
                        <option value="Enterobacter_cloacae">Enterobacter_cloacae</option>
                        <option value="Enterococcus_faecalis">Enterococcus_faecalis</option>
                        <option value="Enterococcus_faecium">Enterococcus_faecium</option>
                        <option value="Escherichia">Escherichia</option>
                        <option value="Klebsiella_aerogenes">Klebsiella_aerogenes</option>
                        <option value="Klebsiella_oxytoca">Klebsiella_oxytoca</option>
                        <option value="Klebsiella_pneumoniae">Klebsiella_pneumoniae</option>
                        <option value="Neisseria_gonorrhoeae">Neisseria_gonorrhoeae</option>
                        <option value="Neisseria_meningitidis">Neisseria_meningitidis</option>
                        <option value="Pseudomonas_aeruginosa">Pseudomonas_aeruginosa</option>
                        <option value="Salmonella">Salmonella</option>
                        <option value="Serratia_marcescens">Serratia_marcescens</option>
                        <option value="Staphylococcus_aureus">Staphylococcus_aureus</option>
                        <option value="Staphylococcus_pseudintermedius">Staphylococcus_pseudintermedius</option>
                        <option value="Streptococcus_agalactiae">Streptococcus_agalactiae</option>
                        <option value="Streptococcus_pneumoniae">Streptococcus_pneumoniae</option>
                        <option value="Streptococcus_pyogenes">Streptococcus_pyogenes</option>
                        <option value="Vibrio_cholerae">Vibrio_cholerae</option>
                    </param>
                    <param argument="--mutation_all" type="boolean" truevalue="--mutation_all" falsevalue="" label="Report genotypes at all locations screened for point mutations"/>
                    <param argument="--report_common"  type="boolean" truevalue="--report_common" falsevalue=""
                    label="Report proteins common to a taxonomy group (need the plus and organism options)"/> 
                </when>
                <when value=""/>
            </conditional>
        </section>
            <!-- OPTIONS -->
        <section name="options" title="Options">
            <param argument="--ident_min" type="float" min="-1" max="1" value="-1" label="Minimum identity" 
            help="Minimum proportion of identical amino acids in alignment. -1 means use a curated threshold if it exists and 0.9 otherwise (default: -1)"/>
            <param argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage" 
            help="Minimum coverage of the reference protein (0 to 1, default: 0.5)"/>
            <param argument="--translation_table"  type="select" optional="true" label="Translation table" help="NCBI genetic code for translated BLAST (default: bacterial table 11)">
                <option value="1">1 Standard code</option>
                <option value="2">2 Vertebrate mitochondrial</option>
                <option value="3">3 Yeast mitochondrial</option>
                <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
                <option value="5">5 Invertebrate mitochondrial</option>
                <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
                <option value="9">9 Echinoderm and flatworm mitochondrial</option>
                <option value="10">10 Euplotid nuclear</option>
                <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
                <option value="12">12 Alternative yeast nuclear</option>
                <option value="13">13 Ascidian mitochondrial</option>
                <option value="14">14 Alternative flatworm mitochondrial</option>
                <option value="16">16 Chlorophycean mitochondrial</option>
                <option value="21">21 Trematode Mitochondrial</option>
                <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
                <option value="23">23 Thraustochytrium Mitochondrial</option>
                <option value="24">24 Rhabdopleuridae Mitochondrial</option>
                <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
                <option value="26">26 Pachysolen tannophilus Nuclear</option>
                <option value="27">27 Karyorelict Nuclear</option>
                <option value="28">28 Condylostoma Nuclear</option>
                <option value="29">29 Mesodinium nuclear</option>
                <option value="30">30 Peritrich nuclear</option>
                <option value="31">31 Blastocrithidia nuclear</option>
                <option value="33">33 Cephalodiscidae mitochondrial</option>
            </param>
            <param argument="--plus"  type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report"/>
            <param argument="--report_all_equal" type="boolean" truevalue="--report_all_equal" falsevalue="" label="Report all equally-scoring BLAST and HMM matches"/> 
            <param argument="--print_node" type="boolean" truevalue="--print_node" falsevalue="" label="print hierarchy node (family)"/> 
            <param argument="--name" type="text" label="First column name" help="Text to be added as the first column 'name' to all rows of the report"/> 
        </section>
    </inputs>
    <outputs>
        <data name="amrfinderplus_report" format="tabular" from_work_dir="amrfinderplus_report.tsv" label="${tool.name} on ${on_string}: AMRFinderPlus report"/>
        <data name="mutation_all_report" format="tabular" from_work_dir="mutation_all_report.tsv" label="${tool.name} on ${on_string}: Point mutation report">
            <filter> organism_options['organism_conditionnal']['organism_select'] == "add_organism" and organism_options['organism_conditionnal']['mutation_all'] is True  </filter>
        </data>
        <data name="protein_output" format="fasta" from_work_dir="amrfinderplus_protein_output.fasta" label="${tool.name} on ${on_string}: Protein identified sequences">
            <filter> input_option['input_mode']['input_select'] in ['protein', 'nucl_prot']</filter>
        </data>
        <data name="nucleotide_output" format="fasta" from_work_dir="amrfinderplus_nucleotide_output.fasta" label="${tool.name} on ${on_string}: Nucleotide identified sequences">
            <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] </filter>
        </data>
        <data name="nucleotide_flank5_output" format="fasta" from_work_dir="amrfinderplus_flanking_sequence_output.fasta" 
        label="${tool.name} on ${on_string}: Nucleotide sequences with 5' flanking regions">
            <filter> input_option['input_mode']['input_select'] in ['nucleotide', 'nucl_prot'] and  input_option['input_mode']['nucleotide_flank5_size'] != 0 </filter>
        </data>
    </outputs>
    <tests>  
        <test expect_num_outputs="2"> <!-- TEST_1 simple nucleotide input   -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="nucleotide"/>
                    <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
                </conditional>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="22"/>
                    <has_n_lines n="8"/>
                    <has_text text="optrA"/>
                    <has_text text="WP_063854496"/>
                    <has_text text="WP_063843211"/>
                </assert_contents>
            </output>
            <output name="nucleotide_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="142"/>
                    <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
                    <has_text text="TTGTCCAAAGCC"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--database"/>
                <not_has_text text="test-db,"/>
            </assert_command>
        </test>    
        <test expect_num_outputs="3"> <!-- TEST_2 nucleotide input and full options  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="nucleotide"/>
                    <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
                    <param name="nucleotide_flank5_size" value="150"/>
                </conditional>
            </section>
            <section name="organism_options">
                <conditional name="organism_conditionnal">
                    <param name="organism_select" value="add_organism"/>
                    <param name="organism" value="Enterococcus_faecalis"/>
                    <param name="report_common" value="true"/>
                </conditional>
            </section>
            <section name="options">
                <param name="ident_min" value="0.1"/>
                <param name="coverage_min" value="0.1"/>
                <param name="translation_table"  value="11"/>
                <param name="plus" value="true"/>
                <param name="report_all_equal" value="true"/>
                <param name="print_node" value="true"/>
                <param name="name" value="test_2"/>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="24"/>
                    <has_n_lines n="13"/>
                    <has_text text="optrA"/>
                    <has_text text="WP_063854496"/>
                </assert_contents>
            </output>
            <output name="nucleotide_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="267"/>
                    <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
                    <has_text text="TTGTCCAAAGCC"/>
                </assert_contents>
            </output>
            <output name="nucleotide_flank5_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="298"/>
                    <has_text text=">contig_2:54987-57395 strand:- mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
                    <has_text text="TTGTCCAAAGCC"/>
                </assert_contents>
            </output>
        </test>    
        <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="nucleotide"/>
                    <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
                </conditional>
            </section>
            <section name="organism_options">
                <conditional name="organism_conditionnal">
                    <param name="organism_select" value="add_organism"/>
                    <param name="organism" value="Enterococcus_faecalis"/>
                    <param name="report_common" value="true"/>
                </conditional>
            </section>
            <section name="options">
                <param name="report_all_equal" value="true"/>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="22"/>
                    <has_n_lines n="9"/>
                    <has_text text="optrA"/>
                    <has_text text="WP_063854496"/>
                    <has_text text="WP_063856080"/>
                </assert_contents>
            </output>
            <output name="nucleotide_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="142"/>
                    <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
                    <has_text text="TTGTCCAAAGCC"/>
                </assert_contents>
            </output>
        </test>    
        <test expect_num_outputs="2"> <!-- TEST_4 simple protein input  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="protein"/>
                    <param name="protein_input" value="enterococcus_faecalis.faa"/>
                </conditional>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="18"/>
                    <has_n_lines n="7"/>
                    <has_text text="optrA"/>
                    <has_text text="WP_063854496"/>
                    <has_text text="WP_063856080"/>
                </assert_contents>
            </output>
            <output name="protein_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="49"/>
                    <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
                    <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
                </assert_contents>
            </output>
        </test>    
        <test expect_num_outputs="2"> <!-- TEST_5 protein input and full options to gff3 and bakta  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="protein"/>
                    <param name="protein_input" value="enterococcus_faecalis.faa"/>
                    <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
                    <param name="annotation_format" value="bakta"/>
                </conditional>
            </section>
            <section name="organism_options">
                <conditional name="organism_conditionnal">
                    <param name="organism_select" value="add_organism"/>
                    <param name="organism" value="Enterococcus_faecalis"/>
                    <param name="report_common" value="true"/>
                </conditional>
            </section>
            <section name="options">
                <param name="ident_min" value="0.1"/>
                <param name="coverage_min" value="0.4"/>
                <param name="translation_table" value="11"/>
                <param name="plus" value="true"/>
                <param name="report_all_equal" value="true"/> 
                <param name="print_node" value="true"/> 
                <param name="name" value="test_5"/> 
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="24"/>
                    <has_n_lines n="8"/>
                    <has_text text="optrA"/>
                    <has_text text="IDOBJL_14770"/>
                    <has_text text="WP_063856080"/>
                </assert_contents>
            </output>
            <output name="nucleotide_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="49"/>
                    <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
                    <has_text text="SDYIVLTEIQKSIDDVKRCQGNYF"/>
                </assert_contents>
            </output>
        </test>    
        <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="protein"/>
                    <param name="protein_input" value="PROKKA_05252023.faa"/>
                    <param name="gff_annotation" value="PROKKA_05252023.gff"/>
                    <param name="annotation_format" value="prokka"/>
                </conditional>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="22"/>
                    <has_n_lines n="7"/>
                    <has_text text="FODBOAIN_02586"/>
                    <has_text text="WP_063856395"/>
                </assert_contents>
            </output>
            <output name="protein_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="49"/>
                    <has_text text=">FODBOAIN_02586 optrA ABC-F type ribosomal protection protein OptrA"/>
                    <has_text text="YSNLLLLFSGIIVISWLVTLNVYKHSQRDF"/>
                </assert_contents>
            </output>
        </test>   
        <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="protein"/>
                    <param name="protein_input" value="input_ncbi.faa"/>
                    <param name="gff_annotation" value="annotation_ncbi.gff3"/>
                </conditional>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="22"/>
                    <has_n_lines n="4"/>
                    <has_text text="blaOXA"/>
                    <has_text text="WP_063855540"/>
                </assert_contents>
            </output>
            <output name="protein_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="17"/>
                    <has_text text=">blaOXA-436_partial blaOXA OXA-48 family class D beta-lactamase"/>
                    <has_text text="SSNPDAAPVSS"/>
                </assert_contents>
            </output>
        </test>   
        <test expect_num_outputs="3"> <!-- TEST_8 both protein and nucleotide input  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="nucl_prot"/>
                    <param name="protein_input" value="enterococcus_faecalis.faa"/>
                    <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
                    <param name="gff_annotation" value="enterococcus_faecalis_bakta.gff3"/>
                    <param name="annotation_format" value="bakta"/>
                </conditional>
            </section>
            <section name="organism_options">
                <conditional name="organism_conditionnal">
                    <param name="organism_select" value="add_organism"/>
                    <param name="organism" value="Enterococcus_faecalis"/>
                </conditional>
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="22"/>
                    <has_n_lines n="8"/>
                    <has_text text="IDOBJL_14770"/>
                    <has_text text="WP_063856080"/>
                </assert_contents>
            </output>
            <output name="nucleotide_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="143"/>
                    <has_text text=">contig_26:6581-8545 strand:+ optrA ABC-F type ribosomal protection protein OptrA"/>
                    <has_text text="CTTATCTGTATAG"/>
                </assert_contents>
            </output>
            <output name="protein_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="37"/>
                    <has_text text=">IDOBJL_14770 aph(3')-IIIa aminoglycoside O-phosphotransferase APH(3')-IIIa"/>
                    <has_text text="QEAGAGMSLLNFT"/>
                </assert_contents>
            </output>
        </test>   
        <test expect_num_outputs="4"> <!-- TEST_9 rast annotation and mutation all results  -->
            <section name="input_option">
                <param name="amrfinder_db_select" value="V3.12-2024-05-02.2"/>
                <conditional name="input_mode">
                    <param name="input_select" value="nucl_prot"/>
                    <param name="protein_input" value="e_faecalis_rast.faa"/>
                    <param name="nucleotide_input" value="e_faecalis_rast.fna"/>
                    <param name="gff_annotation" value="e_faecalis_rast.gff"/>
                    <param name="annotation_format" value="rast"/>
                </conditional>
            </section>
            <section name="organism_options">
                <conditional name="organism_conditionnal">
                    <param name="organism_select" value="add_organism"/>
                    <param name="organism" value="Enterococcus_faecalis"/>
                    <param name="mutation_all" value="true"/> 
                </conditional>
            </section>
            <section name="options">
                <param name="ident_min" value="0.1"/>
                <param name="coverage_min" value="0.1"/>
                <param name="plus" value="true"/>
                <param name="print_node" value="true"/> 
                <param name="name" value="test_5"/> 
            </section>
            <output name="amrfinderplus_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="24"/>
                    <has_n_lines n="2"/>
                    <has_text text="MUPIROCIN"/>
                    <has_text text="WP_063854488"/>
                </assert_contents>
            </output>
            <output name="nucleotide_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="40"/>
                    <has_text text=">contig00019:27227-29524 strand:+ mupB mupirocin-resistant isoleucine--tRNA ligase MupB"/>
                    <has_text text="ATCAGTCGTGAAATAGAA"/>
                </assert_contents>
            </output>
            <output name="protein_output" ftype="fasta">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
            <output name="mutation_all_report" ftype="tabular">
                <assert_contents>
                    <has_n_columns n="24"/>
                    <has_n_lines n="5"/>
                    <has_text text="23S_GA375AG"/>
                    <has_text text="NZ_CP04"/>
                </assert_contents>
            </output>
        </test>   
    </tests>
    <help><![CDATA[
        **What it does**
        
        AMRFinderPlus is a tool to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.
            
        **Input file analysis**

        AMRFinderPlus can check in nucleotide and/or protein fasta file
        When protein file is provided, sensitivity is higher if you add an annotation file

        **Organism options**

        With organism informations AMRFinderPlus screens known resistance causing point mutations and blacklisting of common, non-informative genes.

        The **mutation_all** option make a new output file containing all detected variants from the reference sequence.

        This file allows you to distinguish between called point mutations that were the sensitive variant and the point mutations that could not be called because the sequence was not found.

        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Organism option                 | Point mutations  | Blacklisted plus genes      |    Notes                                                   |
        +=================================+==================+=============================+============================================================+
        | Acinetobacter_baumannii         | X                |                             | Use for the A. baumannii-calcoaceticus species complex     |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Burkholderia_cepacia            | X                |                             | Use for the Burkholderia cepacia species complex           |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Burkholderia_pseudomallei       |  X               |                             | Use for the Burkholderia pseudomallei species complex      |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Campylobacter                   |  X               |                             |  Use for C. coli and C. jejuni                             |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Citrobacter_freundii            |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Clostridioides_difficile        |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Enterobacter_cloacae            |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Enterococcus_faecalis           |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Enterococcus_faecium            |  X               |                             | Use for E. hirae                                           |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Escherichia                     |  X               |   X                         | Use for Shigella and Escherichia                           |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Klebsiella_oxytoca              |  X               |   X                         |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Klebsiella_pneumoniae           |  X               |   X                         | Use for K. pneumoniae species complex and K. aerogenes     |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Neisseria_gonorrhoeae           |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Neisseria_meningitidis          |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Pseudomonas_aeruginosa          |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Salmonella                      |  X               |   X                         |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Serratia_marcescens             |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Staphylococcus_aureus           |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Staphylococcus_pseudintermedius | X                |   X                         |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Streptococcus_agalactiae        |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Streptococcus_pneumoniae        |  X               |                             | Use for S. pneumoniae and S. mitis                         |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Streptococcus_pyogenes          |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
        | Vibrio_cholerae                 |  X               |                             |                                                            |
        +---------------------------------+------------------+-----------------------------+------------------------------------------------------------+
 

        **Supplementary options**
            - *nucleotide 5' flanking size* to extract nucleotide matches and a range of nucleotide in 5'
            - *Minimum identity* to choose threshold in amino acids alignemnt. -1 for a high curation threshold.
            - *Minimum coverage* Coverage to protein alignment.
            - *Translation table* by default AMRFinderPlus work on bacteria but can be modified to some other Phyla.
            - *Plus* option provide more information related to virulence, stress response ...

        **Output files**

            AMRFinderPlus can generate some differents files :
                - The AMRFinderPlus report with identified protein, gene and AMR related informations.
                - A report with all detected variants from the reference sequence.
                - The protein and/ort nucleotide matched sequences.
                - Only when nucleotide a nucleotide fasta file could be provided with 5' flanking regions.
   

    ]]></help>
    <expand macro="citations"/>
</tool>