# HG changeset patch
# User iuc
# Date 1761642978 0
# Node ID eaa563bd535ae7fb5929c95b6876e0e1b8c3e69a
# Parent  6d5c8a6ceea03936f66a2aca805266f230cc104c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr commit 722ac223fd675de7cacf37e3236198725a9a64e3

diff -r 6d5c8a6ceea0 -r eaa563bd535a staramr_search.xml
--- a/staramr_search.xml	Tue Sep 09 15:45:23 2025 +0000
+++ b/staramr_search.xml	Tue Oct 28 09:16:18 2025 +0000
@@ -1,9 +1,9 @@
 <tool id="staramr_search" name="staramr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.11.0</token>
-        <token name="@VERSION_SUFFIX@">3</token>
-        <token name="@PROFILE@">22.05</token>
+        <token name="@TOOL_VERSION@">0.11.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">24.1</token>
         <xml name="element_assert" token_name="" token_text="">
             <element name="@NAME@">
                 <assert_contents>
@@ -104,7 +104,7 @@
 #end if
     ]]></command>
     <inputs>
-        <param name="hide_db_build" type="hidden" value="" />
+        <param name="hide_db_build" type="hidden" value=""/>
         <param type="data" name="genomes" format="fasta" multiple="true"/>
         <param name="staramr_db_select" type="select" label="starAMR database">
             <options from_data_table="staramr_database">
@@ -112,12 +112,12 @@
             </options>
         </param>
         <param argument="--pointfinder-organism" type="select" label="Enable scanning for point mutations using the PointFinder database" help="You can select one of the unvalidated PointFinder organisms to use for scanning for point mutations. These have not been fully validated as compatible with staramr so caution is recommended when interpreting results.">
-            <option value="disabled" selected="true">Disable PointFinder</option>                
+            <option value="disabled" selected="true">Disable PointFinder</option>
             <option value="campylobacter">Campylobacter (campylobacter)</option>
             <option value="enterococcus_faecalis">Enterococcus faecalis (enterococcus_faecalis)</option>
             <option value="enterococcus_faecium">Enterococcus faecium (enterococcus_faecium)</option>
-            <option value="escherichia_coli">Escherichia coli (escherichia_coli)</option>      
-            <option value="helicobacter_pylori">Helicobacter pylori (helicobacter_pylori)</option>          
+            <option value="escherichia_coli">Escherichia coli (escherichia_coli)</option>
+            <option value="helicobacter_pylori">Helicobacter pylori (helicobacter_pylori)</option>
             <option value="salmonella">Salmonella (salmonella)</option>
             <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->
             <option value="klebsiella">Unvalidated: Klebsiella (klebsiella) </option>
@@ -127,18 +127,18 @@
             <option value="staphylococcus_aureus">Unvalidated: Staphylococcus aureus (staphylococcus_aureus)</option>
         </param>
         <section name="advanced" title="Advanced options" expanded="false">
-            <param argument="--pid-threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" min="0" max="100" />
-            <param argument="--percent-length-overlap-resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" min="0" max="100" />
-            <param argument="--percent-length-overlap-pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" min="0" max="100" />
-            <param argument="--percent-length-overlap-plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" min="0" max="100" />
-            <param argument="--genome-size-lower-bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" min="0" />
-            <param argument="--genome-size-upper-bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" min="0" />
-            <param argument="--minimum-N50-value" type="integer" label="The minimum N50 value for the quality metrics" value="10000" min="0" />
-            <param argument="--minimum-contig-length" type="integer" label="The minimum contig length for the quality metrics" value="300" min="0" />
-            <param argument="--unacceptable-number-contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000" min="0" />
-            <param argument="--report-all-blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" help="Report all BLAST results (includes overlapping hits, mainly for debugging)" />
-            <param argument="--exclude-negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" />
-            <param argument="--exclude-resistance-phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
+            <param argument="--pid-threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" min="0" max="100"/>
+            <param argument="--percent-length-overlap-resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0" min="0" max="100"/>
+            <param argument="--percent-length-overlap-pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" min="0" max="100"/>
+            <param argument="--percent-length-overlap-plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" min="0" max="100"/>
+            <param argument="--genome-size-lower-bound" type="integer" label="The lower bound for our genome size for the quality metrics" value="4000000" min="0"/>
+            <param argument="--genome-size-upper-bound" type="integer" label="The upper bound for our genome size for the quality metrics" value="6000000" min="0"/>
+            <param argument="--minimum-N50-value" type="integer" label="The minimum N50 value for the quality metrics" value="10000" min="0"/>
+            <param argument="--minimum-contig-length" type="integer" label="The minimum contig length for the quality metrics" value="300" min="0"/>
+            <param argument="--unacceptable-number-contigs" type="integer" label="The number of contigs, under the minimum contig length which is unacceptable for the quality metrics" value="1000" min="0"/>
+            <param argument="--report-all-blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" help="Report all BLAST results (includes overlapping hits, mainly for debugging)"/>
+            <param argument="--exclude-negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue=""/>
+            <param argument="--exclude-resistance-phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue=""/>
             <param argument="--mlst-scheme" type="select" label="MLST Scheme">
                 <option value="auto" selected="true">Automatic</option>
                 <option value="aactinomycetemcomitans">Aggregatibacter actinomycetemcomitans (aactinomycetemcomitans)</option>
@@ -292,21 +292,21 @@
                     <option value="custom">Provide a custom list of AMR genes to exclude</option>
                     <option value="none">Do not exclude any AMR genes</option>
                 </param>
-                <when value="default" />
+                <when value="default"/>
                 <when value="custom">
-                    <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
+                    <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results"/>
                 </when>
-                <when value="none" />
+                <when value="none"/>
             </conditional>
-            <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" optional="true" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" />
+            <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" optional="true" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results"/>
             <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
                 <option value="include_all" selected="true">Include all available database types</option>
                 <option value="gram_positive">Gram Positive</option>
                 <option value="enterobacteriaceae">Enterobacteriaceae</option>
             </param>
         </section>
-        <section name="output_files" title="Selection of the output files" expanded="true" >
-            <param name="output_selection" type="select" display="checkboxes" multiple="true"  label="Output files selection">
+        <section name="output_files" title="Selection of the output files" expanded="true">
+            <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
                 <option value="mlst_table" selected="true">MLST report</option>
                 <option value="summary_table" selected="true">AMR genes/mutations summary</option>
                 <option value="detailed_summary_table" selected="true">AMR genes/mutations/plasmids detailed summary</option>
@@ -316,91 +316,89 @@
                 <option value="settings_output" selected="false">Settings file</option>
                 <option value="excel_output" selected="false">Excel spreadsheet</option>
             </param>
-        </section> 
+        </section>
     </inputs>
     <outputs>
-        <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: MLST report" >
+        <data format="tabular" name="mlst" label="${tool.name} on ${on_string}: MLST report">
             <filter>output_files['output_selection'] and "mlst_table" in output_files['output_selection']</filter>
         </data>
-        <data format="tabular" name="summary" label="${tool.name} on ${on_string}: AMR genes/mutations summary" >
+        <data format="tabular" name="summary" label="${tool.name} on ${on_string}: AMR genes/mutations summary">
             <filter>output_files['output_selection'] and "summary_table" in output_files['output_selection']</filter>
         </data>
-        <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: AMR genes/mutations/plasmids detailed summary" >
+        <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: AMR genes/mutations/plasmids detailed summary">
             <filter>output_files['output_selection'] and "detailed_summary_table" in output_files['output_selection']</filter>
         </data>
-        <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: AMR gene report from ResFinder" >
+        <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: AMR gene report from ResFinder">
             <filter>output_files['output_selection'] and "resfinder_table" in output_files['output_selection']</filter>
         </data>
-        <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: AMR plasmid type report from PlasmidFinder" >
+        <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: AMR plasmid type report from PlasmidFinder">
             <filter>output_files['output_selection'] and "plasmidfinder_table" in output_files['output_selection']</filter>
         </data>
         <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: AMR point mutation report from PointFinder">
-            <filter>output_files['output_selection'] and "pointfinder_table" in output_files['output_selection']</filter>
+            <filter>output_files['output_selection'] and "pointfinder_table" in output_files['output_selection'] and pointfinder_organism != "disabled"</filter>
         </data>
-        <data format="txt" name="settings" label="${tool.name} on ${on_string}: Settings file" >
+        <data format="txt" name="settings" label="${tool.name} on ${on_string}: Settings file">
             <filter>output_files['output_selection'] and "settings_output" in output_files['output_selection']</filter>
         </data>
-        <data format="xlsx" name="excel" from_work_dir="results.xlsx" label="${tool.name} on ${on_string}: Excel spreadsheet" >
+        <data format="xlsx" name="excel" from_work_dir="results.xlsx" label="${tool.name} on ${on_string}: Excel spreadsheet">
             <filter>output_files['output_selection'] and "excel_output" in output_files['output_selection']</filter>
         </data>
         <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: BLAST hits">
-            <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
+            <discover_datasets pattern="__name_and_ext__" directory="staramr_hits"/>
         </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="9"> <!-- TEST_1 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />
-            <param name="pointfinder_organism" value="salmonella" />
+        <test expect_num_outputs="9">
+            <!-- TEST_1 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="salmonella"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,pointfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="16S-rc_gyrA-rc_beta-lactam.fsa" />
+                    <has_text_matching expression="16S-rc_gyrA-rc_beta-lactam.fsa"/>
                 </assert_contents>
             </output>
             <output name="detailed_summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Resistance" />
+                    <has_text_matching expression="Resistance"/>
                 </assert_contents>
             </output>
             <output name="resfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Subclass B1" />
+                    <has_text_matching expression="Subclass B1"/>
                 </assert_contents>
             </output>
             <output name="plasmidfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Length/Total" />
+                    <has_text_matching expression="Length/Total"/>
                 </assert_contents>
             </output>
             <output name="pointfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Predicted Phenotype" />
+                    <has_text_matching expression="Predicted Phenotype"/>
                 </assert_contents>
             </output>
             <output_collection name="blast_hits" type="list" count="2">
@@ -408,356 +406,338 @@
                 <expand macro="element_assert" name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" text="contig_end: 5121, database_gene_start: 1"/>
             </output_collection>
         </test>
-        <test expect_num_outputs="9"> <!-- TEST_2 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="escherichia_coli" />
+        <test expect_num_outputs="9">
+            <!-- TEST_2 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="escherichia_coli"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,pointfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Amoxicillin" />
+                    <has_text_matching expression="Amoxicillin"/>
                 </assert_contents>
             </output>
             <output name="detailed_summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="MLST" />
+                    <has_text_matching expression="MLST"/>
                 </assert_contents>
             </output>
             <output name="resfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Subclass B1" />
+                    <has_text_matching expression="Subclass B1"/>
                 </assert_contents>
             </output>
             <output name="plasmidfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Length/Total" />
+                    <has_text_matching expression="Length/Total"/>
                 </assert_contents>
             </output>
             <output name="pointfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="CGE Predicted Phenotype" />
+                    <has_text_matching expression="CGE Predicted Phenotype"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_3 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_3 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Quality Module Feedback" />
+                    <has_text_matching expression="Quality Module Feedback"/>
                 </assert_contents>
             </output>
             <output name="resfinder" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="blaIMP-42" />
+                    <has_text_matching expression="blaIMP-42"/>
                 </assert_contents>
             </output>
             <output_collection name="blast_hits" type="list" count="1">
                 <expand macro="element_assert" name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" text="database_gene_end: 741"/>
             </output_collection>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_4 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_4 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="listeria_2" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="listeria_2"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="mlst" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="listeria_2" />
+                    <has_text_matching expression="listeria_2"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_5 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_5 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="99.8" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="99.8"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="5220" />
+                    <has_text_matching expression="5220"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_6 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_6 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="99.8" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="99.8"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa" />
+                    <has_text_matching expression="16S_rc_gyrA_rc_beta-lactam_spaces__extra:characters_.fsa"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_7 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_7 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="438" />
+                    <has_text_matching expression="438"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_8 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_8 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="none" />
+                    <param name="exclude_genes_condition" value="none"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Amikacin" />
+                    <has_text_matching expression="Amikacin"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8"> <!-- TEST_9 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_9 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="4000000" />
-                <param name="genome_size_upper_bound" value="6000000" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="4000000"/>
+                <param name="genome_size_upper_bound" value="6000000"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="custom" />
-                    <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
+                    <param name="exclude_genes_condition" value="custom"/>
+                    <param name="exclude_genes_file" value="genes_to_exclude.tsv"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="438" />
+                    <has_text_matching expression="438"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="8">  <!-- TEST_10 -->
-            <param name="hide_db_build" value="true" />
-            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
-            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502" />            
-            <param name="pointfinder_organism" value="disabled" />
+        <test expect_num_outputs="8">
+            <!-- TEST_10 -->
+            <param name="hide_db_build" value="true"/>
+            <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta"/>
+            <param name="staramr_db_select" value="staramr_downloaded_20112024_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502"/>
+            <param name="pointfinder_organism" value="disabled"/>
             <section name="advanced">
-                <param name="pid_threshold" value="98.0" />
-                <param name="percent_length_overlap_resfinder" value="60.0" />
-                <param name="percent_length_overlap_pointfinder" value="95.0" />
-                <param name="percent_length_overlap_plasmidfinder" value="60.0" />
-                <param name="genome_size_lower_bound" value="1" />
-                <param name="genome_size_upper_bound" value="10" />
-                <param name="minimum_N50_value" value="10000" />
-                <param name="minimum_contig_length" value="300" />
-                <param name="unacceptable_number_contigs" value="1000" />
-                <param name="report_all_blast" value="False" />
-                <param name="exclude_negatives" value="False" />
-                <param name="exclude_resistance_phenotypes" value="False" />
-                <param name="mlst_scheme" value="auto" />
+                <param name="pid_threshold" value="98.0"/>
+                <param name="percent_length_overlap_resfinder" value="60.0"/>
+                <param name="percent_length_overlap_pointfinder" value="95.0"/>
+                <param name="percent_length_overlap_plasmidfinder" value="60.0"/>
+                <param name="genome_size_lower_bound" value="1"/>
+                <param name="genome_size_upper_bound" value="10"/>
+                <param name="minimum_N50_value" value="10000"/>
+                <param name="minimum_contig_length" value="300"/>
+                <param name="unacceptable_number_contigs" value="1000"/>
+                <param name="report_all_blast" value="False"/>
+                <param name="exclude_negatives" value="False"/>
+                <param name="exclude_resistance_phenotypes" value="False"/>
+                <param name="mlst_scheme" value="auto"/>
                 <conditional name="exclude_genes">
-                    <param name="exclude_genes_condition" value="default" />
+                    <param name="exclude_genes_condition" value="default"/>
                 </conditional>
-                <conditional name="complex_mutations">
-                    <param name="complex_mutations_condition" value="default" />
-                </conditional>
-                <param name="plasmidfinder_type" value="include_all" />
+                <param name="plasmidfinder_type" value="include_all"/>
             </section>
             <section name="output_files">
                 <param name="output_selection" value="mlst_table,summary_table,detailed_summary_table,resfinder_table,plasmidfinder_table,settings_output,excel_output"/>
             </section>
             <output name="summary" ftype="tabular">
                 <assert_contents>
-                    <has_text_matching expression="Genome length is not within the acceptable length range \[1,10\]" />
+                    <has_text_matching expression="Genome length is not within the acceptable length range \[1,10\]"/>
                 </assert_contents>
             </output>
         </test>