estrain@8: <tool id="amrfinder_gt" name="amrfinder_gt" version="@VERSION@+galaxy1">
estrain@8:     <description>
estrain@8:       identifies AMR genes using either protein annotations or nucleotide sequence.
estrain@8:     </description>
estrain@8:     <macros>
estrain@8:         <token name="@VERSION@">3.8.28</token>
estrain@8:     </macros>
estrain@8:     <requirements>
estrain@8:         <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement>
estrain@8:     </requirements>
estrain@8:     <version_command><![CDATA[amrfinder --version]]></version_command>
estrain@8: 
estrain@8:     <command detect_errors="exit_code"><![CDATA[
estrain@8:     amrfinder
estrain@8:     $plus
estrain@8:     --threads \${GALAXY_SLOTS:-1}
estrain@8:     --database '$amrfinder_databases.fields.path'
estrain@8:     #if $input_selection.input_source_selector == 'nuc'
estrain@8:         -n '$input_selection.fasta_file'
estrain@8:     #elif  $input_selection.input_source_selector == 'pro'
estrain@8:         -p '$input_selection.fasta_file'
estrain@8:         #if $input_selection.gff.use == 'gff_yes'
estrain@8:             -g '$input_selection.gff.gff_file'
estrain@8:         #end if
estrain@8:     #elif  $input_selection.input_source_selector == 'both'   
estrain@8:         -n '$input_selection.nuc_file'
estrain@8:         -p '$input_selection.pro_file'
estrain@8:         #if $input_selection.gff.use == 'gff_yes'
estrain@8:             -g '$input_selection.gff.gff_file'
estrain@8:         #end if
estrain@8:     #end if
estrain@8:     #if str($organism) != 'None'
estrain@8:         -O $organism
estrain@8:     #end if
estrain@8:     -o results.tsv
estrain@8:     $report_common
estrain@8:     #if $mutation_all == "true"
estrain@8:         --mutation_all mutation_all.tsv
estrain@8:     #end if
estrain@8:     $gpipe
estrain@8:     ]]>    </command>
estrain@8: 
estrain@8:     <inputs>
estrain@8:         <conditional name="input_selection">
estrain@8:             <param name="input_source_selector" type="select" label="Input data type">
estrain@8:                 <option value="nuc">Nucleotide</option>
estrain@8:                 <option value="pro">Protein</option>
estrain@8:                 <option value="both">Nucleotide and Protein</option>
estrain@8:             </param>
estrain@8:             <when value="nuc">
estrain@8:                 <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/>
estrain@8:             </when>
estrain@8:             <when value="pro">
estrain@8:                 <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/>
estrain@8:                 <conditional name="gff">
estrain@8:                     <param name="use" type="select" label="Using GFF to get genomic coordinates">
estrain@8:                         <option value="gff_yes">Yes</option>
estrain@8:                         <option value="gff_no" selected="true">No</option>
estrain@8:                     </param>
estrain@8:                     <when value="gff_yes">
estrain@8:                         <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
estrain@8:                     </when>
estrain@8:                     <when value="gff_no">
estrain@8:                     </when>
estrain@8:                 </conditional>
estrain@8:             </when>
estrain@8:             <when value="both">
estrain@8:                 <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/>
estrain@8:                 <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/>
estrain@8:                 <conditional name="gff">
estrain@8:                     <param name="use" type="select" label="Using GFF to get genomic coordinates">
estrain@8:                         <option value="gff_yes">Yes</option>
estrain@8:                         <option value="gff_no" selected="true">No</option>
estrain@8:                     </param>
estrain@8:                     <when value="gff_yes">
estrain@8:                         <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/>
estrain@8:                     </when>
estrain@8:                     <when value="gff_no">
estrain@8:                     </when>
estrain@8:                 </conditional>
estrain@8:             </when>
estrain@8:         </conditional>
estrain@8:                 <!-- DATABASE INPUT-->
estrain@8:         <param name="amrfinder_databases" label="Select a database" type="select">
estrain@8:             <options from_data_table="amrfinder_databases">
estrain@8:                 <validator message="No database is available" type="no_options" />
estrain@8:             </options>
estrain@8:         </param>
estrain@8:         <param name="organism" type="select" optional="true" label="Get organism-specific results">
estrain@8:             <option value="Campylobacter">Campylobacter</option>
estrain@8:             <option value="Escherichia">Escherichia</option>
estrain@8:             <option value="Klebsiella">Klebsiella</option>
estrain@8:             <option value="Salmonella">Salmonella</option>
estrain@8:             <option value="Staphylococcus">Staphylococcus</option>
estrain@8:             <option value="Vibrio">Vibrio</option>
estrain@8:         </param>
estrain@8:         <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" />
estrain@8:         <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" />
estrain@8:         <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" />
estrain@8:         <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" />
estrain@8:         <param name="mutation_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of mutations" />
estrain@8:         <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" />
estrain@8:     </inputs>
estrain@8: 
estrain@8:     <outputs>
estrain@8:         <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/>
estrain@8:         <data name="all_mutations" format="tabular" from_work_dir="mutation_all.tsv" label="${tool.name} on ${on_string}: All Mutations">
estrain@8:             <filter>mutation_all</filter>
estrain@8:         </data>
estrain@8:     </outputs>
estrain@8: 
estrain@8:     <tests>
estrain@8:         <test> <!-- dna input-->
estrain@8:             <param name="input_source_selector" value="nuc"/>
estrain@8:             <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
estrain@8:             <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@8:             <output name="result" file="test_dna.expected" lines_diff="1"/>
estrain@8:         </test>
estrain@8:         <test> <!-- dna input and organism, plus gene-->
estrain@8:             <param name="input_source_selector" value="nuc"/>
estrain@8:             <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
estrain@8:             <param name="organism" value="Escherichia" />
estrain@8:             <param name="plus" value="true" />
estrain@8:             <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@8:             <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
estrain@8:         </test>
estrain@8:         <test> <!-- AA input-->
estrain@8:             <param name="input_source_selector" value="pro"/>
estrain@8:             <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
estrain@8:             <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@8:             <output name="result" file="test_prot.expected" lines_diff="1"/>
estrain@8:         </test>
estrain@8:         <test> <!-- DNA and AA input-->
estrain@8:             <param name="input_source_selector" value="both"/>
estrain@8:             <param name="use" value="gff_yes"/>
estrain@8:             <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
estrain@8:             <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
estrain@8:             <param name="use" value="gff_yes"/>
estrain@8:             <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
estrain@8:             <param name="amrfinder_databases" value="2019-08-27.1" />
estrain@8:             <output name="result" file="test_both.expected" lines_diff="1"/>
estrain@8:         </test>
estrain@8:     </tests>
estrain@8: 
estrain@8: 
estrain@8:     <help><![CDATA[
estrain@8:     This software and the accompanying database are designed to find acquired
estrain@8:     antimicrobial resistance genes in bacterial protein or assembled nucleotide
estrain@8:     sequences as well as known point mutations for several taxa. With
estrain@8:     AMRFinderPlus we have added select members of additional classes of genes
estrain@8:     such as virulence factors, biocide, heat, acid, and metal resistance genes.
estrain@8:     More details: https://github.com/ncbi/amr/wiki
estrain@8:                 ]]>    </help>
estrain@8:     <citations>
estrain@8:         <citation type="doi">10.1101/550707</citation>
estrain@8:     </citations>
estrain@8: 
estrain@8: </tool>