# HG changeset patch
# User nml
# Date 1667842415 0
# Node ID 4d83eccf5f81b4a468946906c2f03a35a46285f1
# Parent  be818ae858e49d1855466e4f03d67964b5207959
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 7483ccd266d271a05704b1eced996a653b50ee84

diff -r be818ae858e4 -r 4d83eccf5f81 staramr_search.xml
--- a/staramr_search.xml	Wed Jun 22 14:44:55 2022 +0000
+++ b/staramr_search.xml	Mon Nov 07 17:33:35 2022 +0000
@@ -1,14 +1,14 @@
 <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@">0.8.0</token>
+        <token name="@VERSION@">0.9.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">staramr</requirement>
 	<!-- The staramr conda package includes the mlst software, but the list of schemes 
 	     changes depending on the version. I specify the exact version here to make sure
              the list of schemes provided is consistent -->
-	<requirement type="package" version="2.22.0">mlst</requirement>
+	<requirement type="package" version="2.23.0">mlst</requirement>
     </requirements>
     <version_command>staramr --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -82,23 +82,27 @@
         <param type="data" name="genomes" format="fasta" multiple="true"/>
         <conditional name="pointfinder_db">
             <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
-                <option value="disabled" selected="true">Disable PointFinder</option>
+                <option value="disabled" selected="true">Disable PointFinder</option>                
+                <option value="campylobacter">Campylobacter</option>
+                <option value="enterococcus_faecalis">enterococcus_faecalis</option>
+                <option value="enterococcus_faecium">enterococcus_faecium</option>
+                <option value="escherichia_coli">escherichia_coli</option>      
+                <option value="helicobacter_pylori">helicobacter_pylori</option>          
                 <option value="salmonella">Salmonella</option>
-                <option value="campylobacter">Campylobacter</option>
                 <option value="custom">Unvalidated</option>
             </param>
 	    <!-- These three values don't have any additional parameters as they are used as-is to control the PointFinder organism -->
 	    <when value="disabled"/>
+        <when value="campylobacter"/>
+        <when value="enterococcus_faecalis"/>
+        <when value="enterococcus_faecium"/>
+        <when value="escherichia_coli"/>
+        <when value="helicobacter_pylori"/>
 	    <when value="salmonella"/>
-	    <when value="campylobacter"/>
 
 	    <!-- This option provides the ability to select among a number of custom/unvalidated PointFinder organisms -->
             <when value="custom">
-                <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="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="enterococcus_faecalis">enterococcus_faecalis</option>
-                    <option value="enterococcus_faecium">enterococcus_faecium</option>
-                    <option value="escherichia_coli" selected="true">escherichia_coli</option>
-                    <option value="helicobacter_pylori">helicobacter_pylori</option>
+                <param name="pointfinder_custom" type="select" label="PointFinder organism (unvalidated)" help="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="klebsiella">klebsiella</option>
                     <option value="mycobacterium_tuberculosis">mycobacterium_tuberculosis</option>
                     <option value="neisseria_gonorrhoeae">neisseria_gonorrhoeae</option>
@@ -328,8 +332,7 @@
         </test>
         <test>
             <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" ftype="fasta" />
-            <param name="use_pointfinder" value="custom" />
-            <param name="pointfinder_custom" value="escherichia_coli" />
+            <param name="use_pointfinder" value="escherichia_coli" />
 
             <output name="summary" file="test1-summary-ecoli.tsv" ftype="tabular" />
             <output name="detailed_summary" file="test1-detailed-summary-ecoli.tsv" ftype="tabular" />
@@ -395,7 +398,7 @@
 staramr
 =======
 
-staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes.
+staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by their respective webservices_) and compiles a summary report of detected antimicrobial resistance genes.
 
 Usage
 -----
@@ -608,7 +611,7 @@
 .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db
 .. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db
 .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db
-.. _webservice: https://cge.food.dtu.dk/services/ResFinder/
+.. _webservices: http://www.genomicepidemiology.org/services/
     ]]></help>
     <citations>
         <citation type="bibtex">
diff -r be818ae858e4 -r 4d83eccf5f81 test-data/genes_to_exclude.tsv
--- a/test-data/genes_to_exclude.tsv	Wed Jun 22 14:44:55 2022 +0000
+++ b/test-data/genes_to_exclude.tsv	Mon Nov 07 17:33:35 2022 +0000
@@ -1,2 +1,2 @@
-#gene_id
+gene_id
 aac(6')-Iaa_1_NC_003197
diff -r be818ae858e4 -r 4d83eccf5f81 test-data/test1-pointfinder-ecoli.tsv
--- a/test-data/test1-pointfinder-ecoli.tsv	Wed Jun 22 14:44:55 2022 +0000
+++ b/test-data/test1-pointfinder-ecoli.tsv	Mon Nov 07 17:33:35 2022 +0000
@@ -1,1 +1,1 @@
-Isolate ID	Gene	Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End
+Isolate ID	Gene	Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Pointfinder Position
diff -r be818ae858e4 -r 4d83eccf5f81 test-data/test1-pointfinder.tsv
--- a/test-data/test1-pointfinder.tsv	Wed Jun 22 14:44:55 2022 +0000
+++ b/test-data/test1-pointfinder.tsv	Mon Nov 07 17:33:35 2022 +0000
@@ -1,3 +1,3 @@
-Isolate ID	Gene	Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End
-16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	spectinomycin	nucleotide	1065	C -> T	99.94	100.00	1544/1544	16S_rrsD	1604	61
-16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	ciprofloxacin I/R, nalidixic acid	codon	67	GCC -> CCC (A -> P)	99.96	100.00	2637/2637	16S_rrsD	4317	1681
+Isolate ID	Gene	Predicted Phenotype	Type	Position	Mutation	%Identity	%Overlap	HSP Length/Total Length	Contig	Start	End	Pointfinder Position
+16S-rc_gyrA-rc_beta-lactam.fsa	16S_rrsD (C1065T)	spectinomycin	nucleotide	1065	C -> T	99.94	100.00	1544/1544	16S_rrsD	1604	61	C1065T
+16S-rc_gyrA-rc_beta-lactam.fsa	gyrA (A67P)	ciprofloxacin I/R, nalidixic acid	codon	67	GCC -> CCC (A -> P)	99.96	100.00	2637/2637	16S_rrsD	4317	1681	A67P