annotate abromics_galaxy_json_extractor.xml @ 8:fe7c0554432c draft

planemo upload for repository https://gitlab.com/ifb-elixirfr/abromics/galaxy-tools commit 11da23216ea90c4177af3baa9fe2984645af44fc

<tool id="abromics_galaxy_json_extractor" name="abromics_galaxy_json_extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Result extractor to json format
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro='edam'/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
    #import re
    abromics_extract --version &&
    mkdir "abromics_extracted_folder" &&
    #*=================================================================
        Paramaters to add Database and tool version if available
    =================================================================*#
    #set $counter = len($tool_section.tools)-1

    #*======================================================
        Loop to include some different tool in one time
    ======================================================*#
    #for $i, $tool in enumerate( $tool_section.tools )
        abromics_extract
        $tool.select_tool.tool_list
        --hid $tool.select_tool.input.hid
        "$tool.select_tool.input"
        --analysis_software_version "$tool.select_tool.analysis_software_version"
        --reference_database_version "$tool.select_tool.reference_database_version"
        #if $tool.select_tool.tool_list == "bakta"
            #if str($tool.select_tool.annotation_tabular_path) != 'None'
                --annotation_tabular_path '$tool.select_tool.annotation_tabular_path'
                --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid'
            #end if
            #if str($tool.select_tool.annotation_genbank_path) != 'None'
                --annotation_genbank_path '$tool.select_tool.annotation_genbank_path'
                --annotation_genbank_hid '$tool.select_tool.annotation_genbank_path.hid'
            #end if
            #if str($tool.select_tool.annotation_embl_path) != 'None'
                --annotation_embl_path '$tool.select_tool.annotation_embl_path'
                --annotation_embl_hid '$tool.select_tool.annotation_embl_path.hid'
            #end if
            #if str($tool.select_tool.contig_sequences_path) != 'None'
                --contig_sequences_path '$tool.select_tool.contig_sequences_path'
                --contig_sequences_hid '$tool.select_tool.contig_sequences_path.hid'
            #end if
            #if str($tool.select_tool.nucleotide_annotation_path) != 'None'
                --nucleotide_annotation_path '$tool.select_tool.nucleotide_annotation_path'
                --nucleotide_annotation_hid '$tool.select_tool.nucleotide_annotation_path.hid'
            #end if
            #if str($tool.select_tool.amino_acid_annotation_path) != 'None'
                --amino_acid_annotation_path '$tool.select_tool.amino_acid_annotation_path'
                --amino_acid_annotation_hid '$tool.select_tool.amino_acid_annotation_path.hid'
            #end if
            #if str($tool.select_tool.summary_result_path) != 'None'
                --summary_result_path '$tool.select_tool.summary_result_path'
                --summary_result_hid '$tool.select_tool.summary_result_path.hid'
            #end if
            #if str($tool.select_tool.gff_file_path) != 'None'
                --gff_file_path "$tool.select_tool.gff_file_path"
                --gff_file_hid "$tool.select_tool.gff_file_path.hid"
            #end if
            #if str($tool.select_tool.hypothetical_protein_path) != 'None'
                --hypothetical_protein_path '$tool.select_tool.hypothetical_protein_path'
                --hypothetical_protein_hid '$tool.select_tool.hypothetical_protein_path.hid'
            #end if
            #if str($tool.select_tool.hypothetical_tabular_path) != 'None'
                --hypothetical_tabular_path '$tool.select_tool.hypothetical_tabular_path'
                --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid'
            #end if
            #if str($tool.select_tool.plot_file_path) != 'None'
                --plot_file_path '$tool.select_tool.plot_file_path'
                --plot_file_hid '$tool.select_tool.plot_file_path.hid'
            #end if
        #elif $tool.select_tool.tool_list == "bandage"
            #if str($tool.select_tool.bandage_plot_path) != 'None'
                --bandage_plot_path '$tool.select_tool.bandage_plot_path'
                --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid'
            #end if
        #elif $tool.select_tool.tool_list == "bracken"
            #if str($tool.select_tool.kraken_report_path) != 'None'
                --kraken_report_path "$tool.select_tool.kraken_report_path"
                --kraken_report_hid "$tool.select_tool.kraken_report_path.hid"
            #end if
                --threshold "$tool.select_tool.threshold"
                --read_len "$tool.select_tool.read_len"
                --level "$tool.select_tool.level"
        #elif $tool.select_tool.tool_list == "fastp"
            #if str($tool.select_tool.trimmed_forward_R1_path) != 'None'
                --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path'
                --trimmed_forward_R1_hid '$tool.select_tool.trimmed_forward_R1_path.hid'
            #end if
            #if str($tool.select_tool.trimmed_reverse_R2_path) != 'None'
                --trimmed_reverse_R2_path '$tool.select_tool.trimmed_reverse_R2_path'
                --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid'
            #end if
            #if str($tool.select_tool.html_report_path) != 'None'
                --html_report_path '$tool.select_tool.html_report_path'
                --html_report_hid '$tool.select_tool.html_report_path.hid'
            #end if
        #elif $tool.select_tool.tool_list == "integronfinder2"
            #if str($tool.select_tool.summary_file_path) != 'None'
                --summary_file_path "$tool.select_tool.summary_file_path"
                --summary_file_hid "$tool.select_tool.summary_file_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "isescan"
            #if str($tool.select_tool.summary_path) != 'None'
                --summary_path '$tool.select_tool.summary_path'
                --summary_hid '$tool.select_tool.summary_path.hid'
            #end if
            #if str($tool.select_tool.annotation_path) != 'None'
                --annotation_path '$tool.select_tool.annotation_path'
                --annotation_hid '$tool.select_tool.annotation_path.hid'
            #end if
            #if str($tool.select_tool.orf_fna_path) != 'None'
                --orf_fna_path "$tool.select_tool.orf_fna_path"
                --orf_fna_hid "$tool.select_tool.orf_fna_path.hid"
            #end if
            #if str($tool.select_tool.orf_faa_path) != 'None'
                --orf_faa_path "$tool.select_tool.orf_faa_path"
                --orf_faa_hid "$tool.select_tool.orf_faa_path.hid"
            #end if
            #if str($tool.select_tool.is_fna_path) != 'None'
                --is_fna_path "$tool.select_tool.is_fna_path"
                --is_fna_hid "$tool.select_tool.is_fna_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "kraken2"
            #if str($tool.select_tool.seq_classification_file_path) != 'None'
                --seq_classification_file_path "$tool.select_tool.seq_classification_file_path"
                --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "plasmidfinder"
            #if str($tool.select_tool.plasmid_result_tabular_path) != 'None'
                --plasmid_result_tabular_path "$tool.select_tool.plasmid_result_tabular_path"
                --plasmid_result_tabular_hid "$tool.select_tool.plasmid_result_tabular_path.hid"
            #end if
            #if str($tool.select_tool.genome_hit_path) != 'None'
                --genome_hit_path "$tool.select_tool.genome_hit_path"
                --genome_hit_hid "$tool.select_tool.genome_hit_path.hid"
            #end if
            #if str($tool.select_tool.plasmid_hit_path) != 'None'
                --plasmid_hit_path "$tool.select_tool.plasmid_hit_path"
                --plasmid_hit_hid "$tool.select_tool.plasmid_hit_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "quast"
            #if str($tool.select_tool.quast_html_path) != 'None'
                --quast_html_path "$tool.select_tool.quast_html_path"
                --quast_html_hid "$tool.select_tool.quast_html_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "recentrifuge"
            #if str($tool.select_tool.rcf_stat_path) != 'None'
                --rcf_stat_path "$tool.select_tool.rcf_stat_path"
                --rcf_stat_hid "$tool.select_tool.rcf_stat_path.hid"
            #end if
            #if str($tool.select_tool.rcf_html_path) != 'None'
                --rcf_html_path "$tool.select_tool.rcf_html_path"
                --rcf_html_hid "$tool.select_tool.rcf_html_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "shovill"
            #if str($tool.select_tool.contig_graph_path) != 'None'
                --contig_graph_path "$tool.select_tool.contig_graph_path"
                --contig_graph_hid "$tool.select_tool.contig_graph_path.hid"
            #end if
            #if str($tool.select_tool.bam_file_path) != 'None'
                --bam_file_path "$tool.select_tool.bam_file_path"
                --bam_file_hid "$tool.select_tool.bam_file_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "staramr"
            #if str($tool.select_tool.mlst_file_path) != 'None'
                --mlst_file_path "$tool.select_tool.mlst_file_path"
                --mlst_file_hid "$tool.select_tool.mlst_file_path.hid"
            #end if
            #if str($tool.select_tool.plasmidfinder_file_path) != 'None'
                --plasmidfinder_file_path "$tool.select_tool.plasmidfinder_file_path"
                --plasmidfinder_file_hid "$tool.select_tool.plasmidfinder_file_path.hid"
            #end if
            #if str($tool.select_tool.pointfinder_file_path) != 'None'
                --pointfinder_file_path "$tool.select_tool.pointfinder_file_path"
                --pointfinder_file_hid "$tool.select_tool.pointfinder_file_path.hid"
            #end if
            #if str($tool.select_tool.setting_file_path) != 'None'
                --setting_file_path "$tool.select_tool.setting_file_path"
                --setting_file_hid "$tool.select_tool.setting_file_path.hid"
            #end if
        #elif $tool.select_tool.tool_list == "tabular_file"
                --analysis_software_name "$tool.select_tool.analysis_software_name"
        #end if
        -o "abromics_extracted_folder/$($tool.select_tool.tool_list)_$(i)_output.json"
        | tee "$logfile"
        #if $i < $counter
            &&
        #end if
    #end for
        ]]>
    </command>
    <inputs>
        <section name="tool_section" title="Available tools" expanded="true">
            <repeat name="tools" title="Tool" min="0">
                <conditional name="select_tool">
                    <param name="tool_list" type="select" label="Available tools">
                        <option value="abricate">abricate</option>
                        <option value="bakta">bakta</option>
                        <option value="bandage">bandage</option>
                        <option value="bracken">bracken</option>
                        <option value="fastp">fastp</option>
                        <option value="integronfinder2">integronfinder2</option>
                        <option value="isescan">isescan</option>
                        <option value="kraken2">kraken2</option>
                        <option value="multiqc">MultiQC</option>
                        <option value="plasmidfinder">plasmidfinder</option>
                        <option value="quast">quast</option>
                        <option value="recentrifuge">recentrifuge</option>
                        <option value="refseqmasher">refseqmasher</option>
                        <option value="shovill">shovill</option>
                        <option value="staramr">staramr</option>
                        <option value="tabular_file">tabular_generic_file</option>
                    </param>
                    <when value="abricate">
                        <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="bakta">
                        <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/>
                        <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/>
                        <param argument="--annotation_genbank_path" type="data" format="txt" multiple="false" optional="true" label="Bakta genbank file" help="Genbank annotation file"/>
                        <param argument="--annotation_embl_path" type="data" format="txt" multiple="false" optional="true" label="Bakta embl file" help="EMBL annotation file"/>
                        <param argument="--contig_sequences_path" type="data" format="fasta" multiple="false" optional="true" label="Contig sequences" help="Contig sequences files"/>
                        <param argument="--hypothetical_protein_path" type="data" format="fasta" multiple="false" optional="true" label="Hypothetical protein" help="Hypothetical protein fasta file"/>
                        <param argument="--hypothetical_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Hypothetical annotation" help="Hypothetical protein annotation"/>
                        <param argument="--plot_file_path" type="data" format="svg" multiple="false" optional="true" label="Plot file" help="Plot of the annotation in svg format"/>
                        <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/>
                        <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide annotation" help="Nucleotide sequence annotation file"/>
                        <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta protein annotation" help="Amino acid sequence annotation file"/>
                        <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file in gff"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="bandage">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/>
                        <param argument="--bandage_plot_path" type="data" format="svg" multiple="false" optional="true" label="Bandage plot" help="Bandage visualisation file"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="bracken">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                        <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
                        <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
                        <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/>
                        <param argument="--level" type="select" label="Taxonomic level estimation" optional="true" help="Level of final abundance (from Domain to subspecies, default on species)">
                            <option value="D">Domain</option>
                            <option value="P">Phylum</option>
                            <option value="C">Class</option>
                            <option value="O">Order</option>
                            <option value="F">Family</option>
                            <option value="G">Genus</option>
                            <option value="S">Species</option>
                            <option value="S+">Subspecies</option>
                        </param>
                    </when>
                    <when value="fastp">
                        <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
                        <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/>
                        <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/>
                        <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="integronfinder2">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
                        <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Summary report" help="Summary file from integronfinder2"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="isescan">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/>
                        <param argument="--summary_path" type="data" format="tabular" optional="true" multiple="false" label="summary file" help="ISEscan summary"/>
                        <param argument="--annotation_path" type="data" format="gff" optional="true" multiple="false" label="annotation results" help="Annotation in gff file format"/>
                        <param argument="--orf_fna_path" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
                        <param argument="--orf_faa_path" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
                        <param argument="--is_fna_path" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="kraken2">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/>
                        <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="multiqc">
                        <param name="input" type="data" format="html" multiple="false" label="MultiQC report" help="Html report from MultiQC"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="plasmidfinder">
                        <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
                        <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/>
                        <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
                        <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="quast">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
                        <param argument="--quast_html_path" type="data" format="html" multiple="false" optional="true" label="Quast html report" help="Quast html report"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="recentrifuge">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/>
                        <param argument="--rcf_stat_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/>
                        <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="refseqmasher">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="shovill">
                        <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/>
                        <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/>
                        <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="staramr">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/>
                        <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/>
                        <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/>
                        <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/>
                        <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                    <when value="tabular_file">
                        <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
                        <param argument="--analysis_software_name" type="text" multiple="false" optional="true" label="Tool name" help="Tool name which generated the result file"/>
                        <expand macro="analysis_software_version"/>
                        <expand macro="reference_database_version"/>
                    </when>
                </conditional>
            </repeat>
        </section>
        <param name="log" type="boolean" truevalue="true"  falsevalue="" label="Add log" help="Activate/Deactivate the log"/>
    </inputs>
    <outputs>
        <collection name="output_json" type="list" label="${tool.name} on ${on_string}: abromics formated json results">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="abromics_extracted_folder" />
        </collection>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file">
            <filter> log == True </filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile -->
            <section name="tool_section">
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="abricate"/>
                        <param name="input" value="abricate/report.tsv" ftype="tabular"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="2.0" />
                    </conditional>
                </repeat>
            </section>
            <param name="log" value="true"/>
            <output_collection name="output_json" type="list">
                <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
            </output_collection>
            <output name="logfile" value="abricate_logfile.txt"/>
        </test>
        <test expect_num_outputs="1"> <!-- TEST_2 bakta all files -->
            <section name="tool_section">
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="bakta"/>
                        <param name="input" value="bakta/bakta.json" ftype="json"/>
                        <param name="annotation_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="annotation_genbank_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="annotation_embl_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="contig_sequences_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="hypothetical_protein_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="hypothetical_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/>
                        <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
                        <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
                        <param name="analysis_software_version" value="1.8.1"/>
                        <param name="reference_database_version" value="5.0"/>
                    </conditional>
                </repeat>
            </section>
            <output_collection name="output_json" type="list" count="1">
                <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- TEST_3 bakta with no files -->
            <section name="tool_section">
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="bakta"/>
                        <param name="input" value="bakta/bakta.json" ftype="json"/>
                    </conditional>
                </repeat>
            </section>
            <output_collection name="output_json" type="list" count="1">
                <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1"> <!-- TEST_4 All tool in repeat -->
            <section name="tool_section">
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="abricate"/>
                        <param name="input" value="abricate/report.tsv" ftype="tabular"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="2.0" />
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="bakta"/>
                        <param name="input" value="bakta/bakta.json" ftype="json"/>
                        <param name="annotation_tabular_path" value="bakta/bakta_annotation.tsv" ftype="tabular"/>
                        <param name="annotation_genbank_path" value="bakta/bakta_gbff.gbff"/>
                        <param name="annotation_embl_path" value="bakta/bakta_embl.embl"/>
                        <param name="contig_sequences_path" value="bakta/bakta_contigs_sequences.fna" ftype="fasta"/>
                        <param name="hypothetical_protein_path" value="bakta/bakta_hypothetical.faa" ftype="fasta"/>
                        <param name="hypothetical_tabular_path" value="bakta/bakta_hypothetical.tsv" ftype="tabular"/>
                        <param name="plot_file_path" value="bakta/bakta_plot.svg"/>
                        <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/>
                        <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/>
                        <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/>
                        <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/>
                        <param name="analysis_software_version" value="1.8.1"/>
                        <param name="reference_database_version" value="5.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="bandage"/>
                        <param name="input" value="bandage/bandage_info.txt" ftype="txt"/>
                        <param name="bandage_plot_path" value="bandage/bandage_plot.svg"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="bracken"/>
                        <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/>
                        <param name="kraken_report_path" value="bracken/bracken_kraken_report.tsv"/>
                        <param name="read_len" value="100"/>
                        <param name="level" value="S"/>
                        <param name="threshold" value="1"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="fastp"/>
                        <param name="input" value="fastp/fastp_report.json" ftype="json"/>
                        <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/>
                        <param name="trimmed_reverse_R2_path" value="fastp/trimmed_R2.fastq.gz"/>
                        <param name="html_report_path" value="fastp/fastp_report.html"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="integronfinder2"/>
                        <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/>
                        <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>

                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="isescan"/>
                        <param name="input" value="isescan/results.tsv" ftype="tabular"/>
                        <param name="summary_path" value="isescan/summary.tsv"/>
                        <param name="annotation_path" value="isescan/annotation.gff"/>
                        <param name="orf_fna_path" value="isescan/orf.fna"/>
                        <param name="orf_faa_path" value="isescan/orf.faa"/>
                        <param name="is_fna_path" value="isescan/is.fna"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="kraken2"/>
                        <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/>
                        <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="plasmidfinder"/>
                        <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/>
                        <param name="genome_hit_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
                        <param name="plasmid_hit_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="quast"/>
                        <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>
                        <param name="quast_html_path" value="quast/quast_report.html"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="recentrifuge"/>
                        <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>
                        <param name="rcf_stat_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>
                        <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="refseqmasher"/>
                        <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="shovill"/>
                        <param name="input" value="shovill/contigs.fa" ftype="fasta"/>
                        <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>
                        <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="staramr"/>
                        <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/>
                        <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/>
                        <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/>
                        <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/>
                        <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
                <repeat name="tools">
                    <conditional name="select_tool">
                        <param name="tool_list" value="tabular_file"/>
                        <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>
                        <param name="analysis_software_name" value="test_galaxy"/>
                        <param name="analysis_software_version" value="1.0"/>
                        <param name="reference_database_version" value="1.0"/>
                    </conditional>
                </repeat>
            </section>
            <output_collection name="output_json" type="list" count="15">
                <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/>
                <expand macro="element_assert" name="bakta_1_output" text="UniRef50_A0A0H2ZNL3"/>
                <expand macro="element_assert" name="bandage_2_output" text="3042326"/>
                <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/>
                <expand macro="element_assert" name="fastp_4_output" text="705053822"/>
                <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/>
                <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/>
                <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis_ATCC_29212"/>
                <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS12"/>
                <expand macro="element_assert" name="quast_9_output" text="2944723"/>
                <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/>
                <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/>
                <expand macro="element_assert" name="shovill_12_output" text="436224"/>
                <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/>
                <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/>
            </output_collection>
        </test>

    </tests>
    <help><![CDATA[**What it does**
        ** Tool input**
        abromics_galaxy_json_extractor can use several input type from at least 14 different tools :

        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Tools          | Version        | Default input file| Optional files                                             |
        +================+================+===================+============================================================+
        | Abricate       | 1.0.1          |  output.tsv       |                                                            |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Bakta          | 1.7.0          |  output.json      | protein.faa, nucleotide.fna, annotation.gff3, summary.txt  |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Bandage        | 0.8.1          |  info.txt         |                                                            |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Bracken        | 2.8            |  output.tsv       | taxonomy.tsv                                               |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Fastp          | 0.23.2         |  output.json      |                                                            |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Integronfinder2| 2.0.2          |  output.integrons | output.summary                                             |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | ISEScan        | 1.7.2.3        |  output.tsv       | is.fna, orf.faa, orf.fna                                   |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Kraken2        | 2.1.2          |  taxonomy.tsv     | reads_assignation.txt                                      |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Plasmidfinder  | 2.1.6          |  output.json      | genome_hits.fasta, plasmid_hits.fasta                      |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Quast          | 5.2.0          |  output.tsv       |                                                            |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Recentrifuge   | 1.10.0         |  data.tsv         | report.html, stat.tsv                                      |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Refseqmasher   | 0.1.2          |  output.tsv       |                                                            |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Shovill        | 1.1.0          |  contigs.fasta    | alignment.bam, contigs.gfa                                 |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | Staramr        | 0.9.1          |  resfinder.tsv    | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |
        +----------------+----------------+-------------------+------------------------------------------------------------+
        | tabular_file   |  0             |  output.tsv       | no optional files                                          |
        +----------------+----------------+-------------------+------------------------------------------------------------+

        ** Options **
        You can add a tool version and a database version for related tools.
        For some tools you can add optional files previously produced by the tool

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