diff staramr_search.xml @ 17:141afacabcfa draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit e752f6e09372d3513de79d85baa619c5f5065303

--- a/staramr_search.xml	Mon Nov 07 17:33:35 2022 +0000
+++ b/staramr_search.xml	Thu Aug 31 15:55:49 2023 +0000
@@ -1,7 +1,7 @@
 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy0" profile="16.04">
     <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
     <macros>
-        <token name="@VERSION@">0.9.1</token>
+        <token name="@VERSION@">0.10.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">staramr</requirement>
@@ -53,6 +53,11 @@
             --no-exclude-genes
         #end if
 
+
+        #if str($advanced.complex_mutations.complex_mutations_condition) == 'custom'
+	    --complex-mutations-file '${advanced.complex_mutations.complex_mutations_file}'
+	#end if
+
         #if str($advanced.plasmidfinder_type) != 'include_all'
             --plasmidfinder-database-type '${advanced.plasmidfinder_type}'
         #end if
@@ -292,6 +297,16 @@
                     <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" />
+       	    </conditional>
+            <conditional name="complex_mutations">
+                <param name="complex_mutations_condition" type="select" label="Provide a custom list of complex mutations">
+                    <option value="default" selected="true">Use default list of complex mutations</option>
+		    <option value="custom">Provide a custom list of complex mutations</option>
+                </param>
+                <when value="default" />
+                <when value="custom">
+                    <param type="data" name="complex_mutations_file" format="txt,tabular" label="Complex mutations file" help="Pass a file containing a list of complex mutations to group (if present) in the PointFinder results" />
+                </when>
             </conditional>
             <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type">
                 <option value="include_all" selected="true">Include all available database types</option>
@@ -316,7 +331,7 @@
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="9">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <param name="use_pointfinder" value="salmonella" />
 
@@ -324,13 +339,13 @@
             <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" />
             <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" />
             <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
-            <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
+	    <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" />
             <output_collection name="blast_hits" type="list">
                 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
                 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="9">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <param name="use_pointfinder" value="escherichia_coli" />
 
@@ -340,7 +355,7 @@
             <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" />
             <output name="pointfinder" file="test1-pointfinder-ecoli.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
 
             <output name="summary" file="test2-summary.tsv" ftype="tabular" />
@@ -349,44 +364,44 @@
                 <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test2-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             </output_collection>
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <section name="advanced">
                 <param name="mlst_scheme" value="listeria_2" />
             </section>
             <output name="mlst" file="mlst.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
             <param name="pid_threshold" value="99.8" />
 
             <output name="summary" file="test3-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="16S rc_gyrA rc_beta-lactam spaces (extra:characters).fsa" ftype="fasta" />
             <param name="pid_threshold" value="99.8" />
 
             <output name="summary" file="test4-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+	<test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
 
             <output name="summary" file="test5-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
             <param name="exclude_genes_condition" value="none" />
 
             <output name="summary" file="test6-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
             <param name="exclude_genes_condition" value="custom" />
             <param name="exclude_genes_file" value="genes_to_exclude.tsv" />
 
             <output name="summary" file="test5-summary.tsv" ftype="tabular" />
         </test>
-        <test>
+        <test expect_num_outputs="8">
             <param name="genomes" value="test-aminoglycoside.fsa" ftype="fasta" />
             <param name="genome_size_lower_bound" value="1" />
             <param name="genome_size_upper_bound" value="10" />