--- a/abromics_galaxy_json_extractor.xml	Sun Jun 04 17:16:20 2023 +0000
+++ b/abromics_galaxy_json_extractor.xml	Wed Jul 05 14:24:55 2023 +0000
@@ -8,68 +8,185 @@
     <expand macro='edam'/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+    #import re
+    mkdir "abromics_extracted_folder" &&
+    #*=================================================================
+        Paramaters to add Database and tool version if available
+    =================================================================*#
+    #set $counter = len($tool_section.tools)-1
 
-    <command detect_errors="aggressive"><![CDATA[
-        mkdir "abromics_extracted_folder" &&
-#*=================================================================
-    Paramaters to add Database and tool version if available
-=================================================================*#
-#set $software_with_database = str("abricate,bakta,bracken,kraken2,plasmidfinder,recentrifuge").split(",")
-#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 "$tool.select_tool.analysis_software_version"
-    #if str($tool.select_tool.tool_list) in str($software_with_database)
+    #*======================================================
+        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"
-    #end if
-    #if "$tool.select_tool.tool_list" == "bakta"
-        --summary_result_path "$tool.select_tool.summary_result_path"
-        --nucleotide_annotation_path "$tool.select_tool.nucleotide_annotation_path"
-        --amino_acid_annotation_path "$tool.select_tool.amino_acid_annotation_path"
-        --gff_file_path "$tool.select_tool.gff_file_path"
-    #elif "$tool.select_tool.tool_list" == "bracken"
-        --kraken_report_path "tool.select_tool.kraken_report_path"
-        --threshold "tool.select_tool.threshold"
-        --read_length "tool.select_tool.read_length"
-        --level "tool.select_tool.level"
-    #elif"$tool.select_tool.tool_list" == "integronfinder2"
-        --summary_file_path "tool.select_tool.summary_file_path"
-    #elif "$tool.select_tool.tool_list" == "isescan"
-        --orf_fna_file "tool.select_tool.orf_fna_file"
-        --orf_faa_file "tool.select_tool.orf_faa_file"
-        --is_fna_file "tool.select_tool.is_fna_file"
-    #elif "$tool.select_tool.tool_list" == "kraken2"
-        --seq_classification_file_path "tool.select_tool.seq_classification_file_path"
-    #elif "$tool.select_tool.tool_list" == "plasmidfinder"
-        --genome_hit_file_path "tool.select_tool.genome_hit_file_path"
-        --plasmid_sequence_file_path "tool.select_tool.plasmid_sequence_file_path"
-    #elif "$tool.select_tool.tool_list" == "recentrifuge"
-        --rcf_stat_file_path "tool.select_tool.rcf_stat_file_path"
-        --rcf_html_path "tool.select_tool.rcf_html_path"
-    #elif "$tool.select_tool.tool_list" == "shovill"
-        --contig_graph_path "tool.select_tool.contig_graph_path"
-        --bam_file_path "tool.select_tool.bam_file_path"
-    #elif "$tool.select_tool.tool_list" == "staramr"
-        --mlst_file_path "tool.select_tool.mlst_file_path"
-        --plasmidfinder_file_path "tool.select_tool.plasmidfinder_file_path"
-        --pointfinder_file_path "tool.select_tool.pointfinder_file_path"
-        --setting_file_path "tool.select_tool.setting_file_path"
-    #elif "$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
-
+        #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.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 "$tool.select_tool.mlst_file_path"
+                --mlst_hid "$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_hid "$tool.select_tool.plasmidfinder_file_path.hid"
+            #end if
+            #if str($tool.select_tool.pointfinder_file_path) != 'None'
+                --pointfinder_file_path "$tool.select_tool.pointfinder_file_path"
+                --pointfinder_hid "$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_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
+        && ls abromics_extracted_folder 
         ]]>
     </command>
     <inputs>
@@ -85,6 +202,7 @@
                         <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>
@@ -100,16 +218,25 @@
                     </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="Contig sequences" help="Contig sequences files"/>
                         <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 file" help="Nucleotide sequence annotation file"/>
-                        <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta amino acide file" help="Amino acid sequence annotation file"/>
+                        <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"/>
                         <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"/>
@@ -117,7 +244,7 @@
                         <expand macro="reference_database_version"/>
                         <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" 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_length" type="integer" min="0" optional="true" label="Read length"/>
+                        <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/>
                         <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
                             <option value="D">Domain</option>
                             <option value="P">Phylum</option>
@@ -131,19 +258,27 @@
                     </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" 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" 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="--orf_fna_file" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/>
-                        <param argument="--orf_faa_file" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/>
-                        <param argument="--is_fna_file" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/>
+                        <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"/>
@@ -151,20 +286,27 @@
                         <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="--genome_hit_file_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
-                        <param argument="--plasmid_sequence_file_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
+                        <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" 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_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat 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"/>
@@ -172,13 +314,14 @@
                     <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"/>
@@ -187,11 +330,13 @@
                         <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" label="Tool name" help="Tool name which generated the result file"/>
                         <expand macro="analysis_software_version"/>
+                        <expand macro="reference_database_version"/>
                     </when>
                 </conditional>
             </repeat>
@@ -230,11 +375,18 @@
                     <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.fasta" ftype="fasta"/>
+                        <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="reference_database_version" value="1.6.1"/>
+                        <param name="analysis_software_version" value="1.8.1"/>
+                        <param name="reference_database_version" value="5.0"/>
                     </conditional>
                 </repeat>
             </section>
@@ -242,7 +394,20 @@
                 <expand macro="element_assert" name="bakta_0_output" text="UniRef50_A0A0H2ZNL3"/>
             </output_collection>
         </test>
-        <test expect_num_outputs="1"> <!-- TEST_3 All tool in repeat -->
+        <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">
@@ -256,28 +421,51 @@
                     <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="bracken/bracken_kraken_report" ftype="tabular" />
-                        <param name="threshold" value="0" />
-                        <param name="read_length" value="100"/>
+                        <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">
@@ -285,15 +473,22 @@
                         <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="orf_fna_file" value="isescan/orf.fna" ftype="fasta"/>
-                        <param name="orf_faa_file" value="isescan/orf.faa" ftype="fasta"/>
-                        <param name="is_fna_file" value="isescan/is.fna" ftype="fasta"/>
+                        <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">
@@ -301,34 +496,45 @@
                         <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_file_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/>
-                        <param name="plasmid_sequence_file_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/>
+                        <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_file_path" value="recentrifuge/rcf_stat.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">
@@ -337,6 +543,8 @@
                         <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">
@@ -347,12 +555,17 @@
                         <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>
@@ -374,10 +587,12 @@
                 <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       |                                                            |