--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amrfinderplus.xml	Fri May 26 09:18:37 2023 +0000
@@ -0,0 +1,453 @@
+<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='edam'/>
+    <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_database">
+                  <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="">
+                </when>
+            </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="V3.11.1-2023-04-17.1"/>
+                <conditional name="input_mode">
+                    <param name="input_select" value="nucleotide"/>
+                    <param name="nucleotide_input" value="enterococcus_faecalis.fna"/>
+                </conditional>
+            </section>
+            <output name="amrfinderplus_report" value="test_1/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="nucleotide_output" value="test_1/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>    
+        <test expect_num_outputs="4"> <!-- TEST_2 nucleotide input and full options  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <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="mutation_all" value="true"/>
+                    <param name="report_common" value="true"/>
+                </conditional>
+            </section>
+            <section name="options">
+                <param name="ident_min" value="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"/>
+                <param name="log"  value="true"/>
+            </section>
+            <output name="amrfinderplus_report" value="test_2/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="mutation_all_report" value="test_2/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="nucleotide_output" value="test_2/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>
+            <output name="nucleotide_flank5_output" value="test_2/amrfinderplus_flanking_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>    
+        <test expect_num_outputs="2"> <!-- TEST_3 nucleotide input and several options  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <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" value="test_3/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="nucleotide_output" value="test_3/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>    
+        <test expect_num_outputs="2"> <!-- TEST_4 simple protein input  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <conditional name="input_mode">
+                    <param name="input_select" value="protein"/>
+                    <param name="protein_input" value="enterococcus_faecalis.faa"/>
+                </conditional>
+            </section>
+            <output name="amrfinderplus_report" value="test_4/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="protein_output" value="test_4/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>    
+        <test expect_num_outputs="3"> <!-- TEST_5 protein input and full options to gff3 and bakta  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <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="mutation_all" value="true"/>
+                    <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" value="test_5/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="mutation_all_report" value="test_5/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="protein_output" value="test_5/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>    
+        <test expect_num_outputs="2"> <!-- TEST_6 protein input and prokka annotation  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <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" value="test_6/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="protein_output" value="test_6/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>   
+        <test expect_num_outputs="2"> <!-- TEST_7 protein input and genbank default annotation  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <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" value="test_7/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="protein_output" value="test_7/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/>
+        </test>   
+        <test expect_num_outputs="4"> <!-- TEST_8 both protein and nucleotide input  -->
+            <section name="input_option">
+                <param name="amrfinder_db_select" value="V3.11.1-2023-04-17.1"/>
+                <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"/>
+                    <param name="mutation_all" value="true"/>
+                    <param name="report_common" value="true"/>
+                </conditional>
+            </section>
+            <output name="amrfinderplus_report" value="test_8/amrfinderplus_results.tsv" ftype="tabular" lines_diff="1"/>
+            <output name="protein_output" value="test_8/amrfinderplus_protein_output.fasta" ftype="fasta" lines_diff="1"/>
+            <output name="nucleotide_output" value="test_8/amrfinderplus_nucleotide_output.fasta" ftype="fasta" lines_diff="1"/>
+            <output name="mutation_all_report" value="test_8/amrfinderplus_mutation_all.tsv" ftype="tabular" lines_diff="1"/>
+        </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>