# HG changeset patch
# User iuc
# Date 1729152015 0
# Node ID ea93df4b3df2dd193e6e01295de03a0b796de28c
# Parent  8d6686664021587271a004154df5efa90bc846bf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 301f4d78613f8f6e120b5ed8b56bd5e084e99b13

diff -r 8d6686664021 -r ea93df4b3df2 macro.xml
--- a/macro.xml	Mon Sep 30 10:15:57 2024 +0000
+++ b/macro.xml	Thu Oct 17 08:00:15 2024 +0000
@@ -1,13 +1,22 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">0.9.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
         <version_command><![CDATA[tooldistillator --version]]></version_command>
     </xml>
     <xml name="analysis_software_version">
-        <param argument="--analysis_software_version" type="text" optional="true" label="Analysis software version"/>
+        <conditional name="origin">
+            <param name="origin" type="select" label="Has the dataset just been imported?">
+                <option value="true">Yes</option>
+                <option value="false">No</option>
+            </param>
+            <when value="true">
+                <param argument="--analysis_software_version" type="text" optional="true" label="Analysis software version"/>
+            </when>
+            <when value="false"/>
+        </conditional>
     </xml>
     <xml name="reference_database_version">
         <param argument="--reference_database_version" type="text" optional="true" label="Database software version"/>
diff -r 8d6686664021 -r ea93df4b3df2 tooldistillator.xml
--- a/tooldistillator.xml	Mon Sep 30 10:15:57 2024 +0000
+++ b/tooldistillator.xml	Thu Oct 17 08:00:15 2024 +0000
@@ -10,204 +10,230 @@
     <expand macro="version_command"/>
     <command detect_errors="aggressive"><![CDATA[
 #import re
+set -x pipefail;
+
 mkdir "tooldistillator_folder" &&
 
 #set $counter = len($tool_section.tools)-1
     #for $i, $tool in enumerate( $tool_section.tools )
+        #if $tool.select_tool.tool_list == 'staramr':
+ln -s '$tool.select_tool.input' 'resfinder.tsv' &&
+            #if $tool.select_tool.mlst_file_path
+ln -s '$tool.select_tool.mlst_file_path' 'mlst.tsv' &&
+            #end if
+            #if $tool.select_tool.plasmidfinder_file_path
+ln -s '$tool.select_tool.plasmidfinder_file_path' 'plasmidfinder.tsv' &&
+            #end if
+            #if $tool.select_tool.pointfinder_file_path
+ln -s '$tool.select_tool.pointfinder_file_path' 'pointfinder.tsv' &&
+            #end if
+            #if $tool.select_tool.setting_file_path
+ln -s '$tool.select_tool.setting_file_path' 'setting.tsv' &&
+            #end if
+        #end if
+
 tooldistillator
-        $tool.select_tool.tool_list
-        --hid '$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'
+    $tool.select_tool.tool_list
+    --hid '$tool.select_tool.input.hid'
+        #if $tool.select_tool.tool_list == 'staramr':
+    'resfinder.tsv'
+        #else
+    '$tool.select_tool.input'
+        #end if
+        #if $tool.select_tool.origin.origin == 'true':
+    --analysis_software_version '$tool.select_tool.origin.analysis_software_version'
+        #else
+    --analysis_software_version '$tool.select_tool.input.creating_job.tool_version'
+        #end if
+    --reference_database_version '$tool.select_tool.reference_database_version'
         #if $tool.select_tool.tool_list == 'amrfinderplus':
             #if $tool.select_tool.point_mutation_report_path
-                --point_mutation_report_path '$tool.select_tool.point_mutation_report_path'
-                --point_mutation_report_hid '$tool.select_tool.point_mutation_report_path.hid'
+    --point_mutation_report_path '$tool.select_tool.point_mutation_report_path'
+    --point_mutation_report_hid '$tool.select_tool.point_mutation_report_path.hid'
             #end if
             #if $tool.select_tool.nucleotide_sequence_path
-                --nucleotide_sequence_path '$tool.select_tool.nucleotide_sequence_path'
-                --nucleotide_sequence_hid '$tool.select_tool.nucleotide_sequence_path.hid'
+    --nucleotide_sequence_path '$tool.select_tool.nucleotide_sequence_path'
+    --nucleotide_sequence_hid '$tool.select_tool.nucleotide_sequence_path.hid'
             #end if
         #elif $tool.select_tool.tool_list == 'bakta'
             #if $tool.select_tool.annotation_tabular_path
-                --annotation_tabular_path '$tool.select_tool.annotation_tabular_path'
-                --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid'
+    --annotation_tabular_path '$tool.select_tool.annotation_tabular_path'
+    --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid'
             #end if
             #if $tool.select_tool.annotation_genbank_path
-                --annotation_genbank_path '$tool.select_tool.annotation_genbank_path'
-                --annotation_genbank_hid '$tool.select_tool.annotation_genbank_path.hid'
+    --annotation_genbank_path '$tool.select_tool.annotation_genbank_path'
+    --annotation_genbank_hid '$tool.select_tool.annotation_genbank_path.hid'
             #end if
             #if $tool.select_tool.annotation_embl_path
-                --annotation_embl_path '$tool.select_tool.annotation_embl_path'
-                --annotation_embl_hid '$tool.select_tool.annotation_embl_path.hid'
+    --annotation_embl_path '$tool.select_tool.annotation_embl_path'
+    --annotation_embl_hid '$tool.select_tool.annotation_embl_path.hid'
             #end if
             #if $tool.select_tool.contig_sequences_path
-                --contig_sequences_path '$tool.select_tool.contig_sequences_path'
-                --contig_sequences_hid '$tool.select_tool.contig_sequences_path.hid'
+    --contig_sequences_path '$tool.select_tool.contig_sequences_path'
+    --contig_sequences_hid '$tool.select_tool.contig_sequences_path.hid'
             #end if
             #if $tool.select_tool.nucleotide_annotation_path
-                --nucleotide_annotation_path '$tool.select_tool.nucleotide_annotation_path'
-                --nucleotide_annotation_hid '$tool.select_tool.nucleotide_annotation_path.hid'
+    --nucleotide_annotation_path '$tool.select_tool.nucleotide_annotation_path'
+    --nucleotide_annotation_hid '$tool.select_tool.nucleotide_annotation_path.hid'
             #end if
             #if $tool.select_tool.amino_acid_annotation_path
-                --amino_acid_annotation_path '$tool.select_tool.amino_acid_annotation_path'
-                --amino_acid_annotation_hid '$tool.select_tool.amino_acid_annotation_path.hid'
+    --amino_acid_annotation_path '$tool.select_tool.amino_acid_annotation_path'
+    --amino_acid_annotation_hid '$tool.select_tool.amino_acid_annotation_path.hid'
             #end if
             #if $tool.select_tool.summary_result_path
-                --summary_result_path '$tool.select_tool.summary_result_path'
-                --summary_result_hid '$tool.select_tool.summary_result_path.hid'
+    --summary_result_path '$tool.select_tool.summary_result_path'
+    --summary_result_hid '$tool.select_tool.summary_result_path.hid'
             #end if
             #if $tool.select_tool.gff_file_path
-                --gff_file_path '$tool.select_tool.gff_file_path'
-                --gff_file_hid '$tool.select_tool.gff_file_path.hid'
+    --gff_file_path '$tool.select_tool.gff_file_path'
+    --gff_file_hid '$tool.select_tool.gff_file_path.hid'
             #end if
             #if $tool.select_tool.hypothetical_protein_path
-                --hypothetical_protein_path '$tool.select_tool.hypothetical_protein_path'
-                --hypothetical_protein_hid '$tool.select_tool.hypothetical_protein_path.hid'
+    --hypothetical_protein_path '$tool.select_tool.hypothetical_protein_path'
+    --hypothetical_protein_hid '$tool.select_tool.hypothetical_protein_path.hid'
             #end if
             #if $tool.select_tool.hypothetical_tabular_path
-                --hypothetical_tabular_path '$tool.select_tool.hypothetical_tabular_path'
-                --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid'
+    --hypothetical_tabular_path '$tool.select_tool.hypothetical_tabular_path'
+    --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid'
             #end if
             #if $tool.select_tool.plot_file_path
-                --plot_file_path '$tool.select_tool.plot_file_path'
-                --plot_file_hid '$tool.select_tool.plot_file_path.hid'
+    --plot_file_path '$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 $tool.select_tool.bandage_plot_path
-                --bandage_plot_path '$tool.select_tool.bandage_plot_path'
-                --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid'
+    --bandage_plot_path '$tool.select_tool.bandage_plot_path'
+    --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid'
             #end if
         #elif $tool.select_tool.tool_list == 'bwa':
             #if $tool.select_tool.paired_second_file_path
-                --paired_second_file_path '$tool.select_tool.paired_second_file_path'
-                --paired_second_file_hid '$tool.select_tool.paired_second_file_path.hid'
+    --paired_second_file_path '$tool.select_tool.paired_second_file_path'
+    --paired_second_file_hid '$tool.select_tool.paired_second_file_path.hid'
             #end if
         #elif $tool.select_tool.tool_list == 'bracken':
             #if $tool.select_tool.kraken_report_path
-                --kraken_report_path '$tool.select_tool.kraken_report_path'
-                --kraken_report_hid '$tool.select_tool.kraken_report_path.hid'
+    --kraken_report_path '$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'
+    --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 $tool.select_tool.trimmed_forward_R1_path
-                --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path'
-                --trimmed_forward_R1_hid '$tool.select_tool.trimmed_forward_R1_path.hid'
+    --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path'
+    --trimmed_forward_R1_hid '$tool.select_tool.trimmed_forward_R1_path.hid'
             #end if
             #if $tool.select_tool.trimmed_reverse_R2_path
-                --trimmed_reverse_R2_path '$tool.select_tool.trimmed_reverse_R2_path'
-                --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid'
+    --trimmed_reverse_R2_path '$tool.select_tool.trimmed_reverse_R2_path'
+    --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid'
             #end if
             #if $tool.select_tool.html_report_path
-                --html_report_path '$tool.select_tool.html_report_path'
-                --html_report_hid '$tool.select_tool.html_report_path.hid'
+    --html_report_path '$tool.select_tool.html_report_path'
+    --html_report_hid '$tool.select_tool.html_report_path.hid'
             #end if
         #elif $tool.select_tool.tool_list == 'fastqc':
             #if $tool.select_tool.html_report_path
-                --html_report_path '$tool.select_tool.html_report_path'
-                --html_report_hid '$tool.select_tool.html_report_path.hid'
+    --html_report_path '$tool.select_tool.html_report_path'
+    --html_report_hid '$tool.select_tool.html_report_path.hid'
             #end if
         #elif $tool.select_tool.tool_list == 'flye':
             #if $tool.select_tool.contig_graph_path
-                --contig_graph_path '$tool.select_tool.contig_graph_path'
-                --contig_graph_hid '$tool.select_tool.contig_graph_path.hid'
+    --contig_graph_path '$tool.select_tool.contig_graph_path'
+    --contig_graph_hid '$tool.select_tool.contig_graph_path.hid'
             #end if
             #if $tool.select_tool.tsv_file_path
-                --tsv_file_path '$tool.select_tool.tsv_file_path'
-                --tsv_file_hid '$tool.select_tool.tsv_file_path.hid'
+    --tsv_file_path '$tool.select_tool.tsv_file_path'
+    --tsv_file_hid '$tool.select_tool.tsv_file_path.hid'
             #end if
         #elif $tool.select_tool.tool_list == 'integronfinder2':
             #if $tool.select_tool.summary_file_path
-                --summary_file_path '$tool.select_tool.summary_file_path'
-                --summary_file_hid '$tool.select_tool.summary_file_path.hid'
+    --summary_file_path '$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 $tool.select_tool.summary_path
-                --summary_path '$tool.select_tool.summary_path'
-                --summary_hid '$tool.select_tool.summary_path.hid'
+    --summary_path '$tool.select_tool.summary_path'
+    --summary_hid '$tool.select_tool.summary_path.hid'
             #end if
             #if $tool.select_tool.annotation_path
-                --annotation_path '$tool.select_tool.annotation_path'
-                --annotation_hid '$tool.select_tool.annotation_path.hid'
+    --annotation_path '$tool.select_tool.annotation_path'
+    --annotation_hid '$tool.select_tool.annotation_path.hid'
             #end if
             #if $tool.select_tool.orf_fna_path
-                --orf_fna_path '$tool.select_tool.orf_fna_path'
-                --orf_fna_hid '$tool.select_tool.orf_fna_path.hid'
+    --orf_fna_path '$tool.select_tool.orf_fna_path'
+    --orf_fna_hid '$tool.select_tool.orf_fna_path.hid'
             #end if
             #if $tool.select_tool.orf_faa_path
-                --orf_faa_path '$tool.select_tool.orf_faa_path'
-                --orf_faa_hid '$tool.select_tool.orf_faa_path.hid'
+    --orf_faa_path '$tool.select_tool.orf_faa_path'
+    --orf_faa_hid '$tool.select_tool.orf_faa_path.hid'
             #end if
             #if $tool.select_tool.is_fna_path
-                --is_fna_path '$tool.select_tool.is_fna_path'
-                --is_fna_hid '$tool.select_tool.is_fna_path.hid'
+    --is_fna_path '$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 $tool.select_tool.seq_classification_file_path
-                --seq_classification_file_path '$tool.select_tool.seq_classification_file_path'
-                --seq_classification_file_hid '$tool.select_tool.seq_classification_file_path.hid'
+    --seq_classification_file_path '$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 $tool.select_tool.plasmid_result_tabular_path
-                --plasmid_result_tabular_path '$tool.select_tool.plasmid_result_tabular_path'
-                --plasmid_result_tabular_hid '$tool.select_tool.plasmid_result_tabular_path.hid'
+    --plasmid_result_tabular_path '$tool.select_tool.plasmid_result_tabular_path'
+    --plasmid_result_tabular_hid '$tool.select_tool.plasmid_result_tabular_path.hid'
             #end if
             #if $tool.select_tool.genome_hit_path
-                --genome_hit_path '$tool.select_tool.genome_hit_path'
-                --genome_hit_hid '$tool.select_tool.genome_hit_path.hid'
+    --genome_hit_path '$tool.select_tool.genome_hit_path'
+    --genome_hit_hid '$tool.select_tool.genome_hit_path.hid'
             #end if
             #if $tool.select_tool.plasmid_hit_path
-                --plasmid_hit_path '$tool.select_tool.plasmid_hit_path'
-                --plasmid_hit_hid '$tool.select_tool.plasmid_hit_path.hid'
+    --plasmid_hit_path '$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 $tool.select_tool.quast_html_path
-                --quast_html_path '$tool.select_tool.quast_html_path'
-                --quast_html_hid '$tool.select_tool.quast_html_path.hid'
+    --quast_html_path '$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 $tool.select_tool.rcf_stat_path
-                --rcf_stat_path '$tool.select_tool.rcf_stat_path'
-                --rcf_stat_hid '$tool.select_tool.rcf_stat_path.hid'
+    --rcf_stat_path '$tool.select_tool.rcf_stat_path'
+    --rcf_stat_hid '$tool.select_tool.rcf_stat_path.hid'
             #end if
             #if $tool.select_tool.rcf_html_path
-                --rcf_html_path '$tool.select_tool.rcf_html_path'
-                --rcf_html_hid '$tool.select_tool.rcf_html_path.hid'
+    --rcf_html_path '$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 $tool.select_tool.contig_graph_path
-                --contig_graph_path '$tool.select_tool.contig_graph_path'
-                --contig_graph_hid '$tool.select_tool.contig_graph_path.hid'
+    --contig_graph_path '$tool.select_tool.contig_graph_path'
+    --contig_graph_hid '$tool.select_tool.contig_graph_path.hid'
             #end if
             #if $tool.select_tool.bam_file_path
-                --bam_file_path '$tool.select_tool.bam_file_path'
-                --bam_file_hid '$tool.select_tool.bam_file_path.hid'
+    --bam_file_path '$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 $tool.select_tool.mlst_file_path
-                --mlst_file_path '$tool.select_tool.mlst_file_path'
-                --mlst_file_hid '$tool.select_tool.mlst_file_path.hid'
+    --mlst_file_path 'mlst.tsv'
+    --mlst_file_hid '$tool.select_tool.mlst_file_path.hid'
             #end if
             #if $tool.select_tool.plasmidfinder_file_path
-                --plasmidfinder_file_path '$tool.select_tool.plasmidfinder_file_path'
-                --plasmidfinder_file_hid '$tool.select_tool.plasmidfinder_file_path.hid'
+    --plasmidfinder_file_path 'plasmidfinder.tsv'
+    --plasmidfinder_file_hid '$tool.select_tool.plasmidfinder_file_path.hid'
             #end if
             #if $tool.select_tool.pointfinder_file_path
-                --pointfinder_file_path '$tool.select_tool.pointfinder_file_path'
-                --pointfinder_file_hid '$tool.select_tool.pointfinder_file_path.hid'
+    --pointfinder_file_path 'pointfinder.tsv'
+    --pointfinder_file_hid '$tool.select_tool.pointfinder_file_path.hid'
             #end if
             #if $tool.select_tool.setting_file_path
-                --setting_file_path '$tool.select_tool.setting_file_path'
-                --setting_file_hid '$tool.select_tool.setting_file_path.hid'
+    --setting_file_path 'setting.tsv'
+    --setting_file_hid '$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'
+    --analysis_software_name '$tool.select_tool.analysis_software_name'
         #end if
-        -o 'tooldistillator_folder/$($tool.select_tool.tool_list)_$(i)_output.json'
-        | tee '$logfile'
+    -o 'tooldistillator_folder/$($tool.select_tool.tool_list)_$(i)_output.json'
+| tee '$logfile'
         #if $i < $counter
             &&
         #end if
@@ -426,7 +452,9 @@
                     <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="false"/>
+                        </conditional>
                         <param name="reference_database_version" value="2.0" />
                     </conditional>
                 </repeat>
@@ -455,7 +483,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.8.1"/>
+                        </conditional>
                         <param name="reference_database_version" value="5.0"/>
                     </conditional>
                 </repeat>
@@ -483,7 +514,10 @@
                     <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="2.0" />
                     </conditional>
                 </repeat>
@@ -493,7 +527,10 @@
                         <param name="input" value="amrfinderplus/AMRFinderPlus_report.tsv" ftype="tabular"/>
                         <param name="point_mutation_report_path" value="amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv" ftype="tabular"/>
                         <param name="nucleotide_sequence_path" value="amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta" ftype="fasta"/>
-                        <param name="analysis_software_version" value="3.11.26"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="3.11.26"/>
+                        </conditional>
                         <param name="reference_database_version" value="v3.11-2023-04-17.1"/>
                     </conditional>
                 </repeat>
@@ -512,7 +549,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.8.1"/>
+                        </conditional>
                         <param name="reference_database_version" value="5.0"/>
                     </conditional>
                 </repeat>
@@ -521,7 +561,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -533,7 +576,10 @@
                         <param name="read_len" value="100"/>
                         <param name="level" value="S"/>
                         <param name="threshold" value="1"/>
-                        <param name="analysis_software_version" value="1.0"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -542,7 +588,10 @@
                         <param name="tool_list" value="bwa"/>
                         <param name="input" value="bwa/aligned_R1.bam" ftype="bam"/>
                         <param name="paired_second_file_path" value="bwa/aligned_R2.bam"/>
-                        <param name="analysis_software_version" value="2.2.1"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="2.2.1"/>
+                        </conditional>
                         <param name="reference_database_version" value="tests/data/dummy/flye/assembly.fasta"/>
                     </conditional>
                 </repeat>
@@ -553,7 +602,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -562,7 +614,10 @@
                         <param name="tool_list" value="fastqc"/>
                         <param name="input" value="fastqc/fastqc_report.txt" ftype="txt"/>
                         <param name="html_report_path" value="fastqc/fastqc_report.html"/>
-                        <param name="analysis_software_version" value="0.12.1"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="0.12.1"/>
+                        </conditional>
                         <param name="reference_database_version" value=""/>
                     </conditional>
                 </repeat>
@@ -570,7 +625,10 @@
                     <conditional name="select_tool">
                         <param name="tool_list" value="filtlong"/>
                         <param name="input" value="filtlong/filtered_sample.fastq.gz" ftype="fastq.gz"/>
-                        <param name="analysis_software_version" value="0.2.1"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="0.2.1"/>
+                        </conditional>
                         <param name="reference_database_version" value=""/>
                     </conditional>
                 </repeat>
@@ -580,7 +638,10 @@
                         <param name="input" value="flye/assembly.fasta" ftype="fasta"/>
                         <param name="contig_graph_path" value="flye/assembly.gfa" ftype="txt"/>
                         <param name="tsv_file_path" value="flye/assembly_infos.tsv" ftype="tabular"/>
-                        <param name="analysis_software_version" value="2.9.1"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="2.9.1"/>
+                        </conditional>
                         <param name="reference_database_version" value=""/>
                     </conditional>
                 </repeat>
@@ -589,7 +650,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -602,7 +666,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -611,7 +678,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -621,7 +691,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -629,7 +702,10 @@
                     <conditional name="select_tool">
                         <param name="tool_list" value="polypolish"/>
                         <param name="input" value="polypolish/polished_assembly.fasta" ftype="fasta"/>
-                        <param name="analysis_software_version" value="0.2.1"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="0.2.1"/>
+                        </conditional>
                         <param name="reference_database_version" value=""/>
                     </conditional>
                 </repeat>
@@ -638,7 +714,10 @@
                         <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="0.5.0"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="0.5.0"/>
+                        </conditional>
                         <param name="reference_database_version" value=""/>
                     </conditional>
                 </repeat>
@@ -648,7 +727,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -656,7 +738,10 @@
                     <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -666,7 +751,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -675,7 +763,10 @@
                         <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"/>
+                        <conditional name="origin">
+                            <param name="origin" value="true"/>
+                            <param name="analysis_software_version" value="1.0"/>
+                        </conditional>
                         <param name="reference_database_version" value="1.0"/>
                     </conditional>
                 </repeat>
@@ -703,7 +794,6 @@
                 <expand macro="element_assert" name="tabular_file_19_output" text="NP_814691"/>
             </output_collection>
         </test>
-
     </tests>
     <help><![CDATA[
 **What it does**