# HG changeset patch
# User nml
# Date 1734551030 0
# Node ID 3548a93b39c1488e0e1a2013b4eacc0b33e82503
# Parent  3b22de20bd4b20357760f002d00d92afb3192609
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit b534dcd63f07469e6e24257a0491a8badcbfc95d

diff -r 3b22de20bd4b -r 3548a93b39c1 staramr_search.xml
--- a/staramr_search.xml	Tue Sep 19 18:41:35 2023 +0000
+++ b/staramr_search.xml	Wed Dec 18 19:43:50 2024 +0000
@@ -1,14 +1,13 @@
-<tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1" profile="16.04">
+<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@">0.10.0</token>
+        <token name="@VERSION@">0.11.0</token>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">staramr</xref>
+    </xrefs>
     <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="2.23.0">mlst</requirement>
     </requirements>
     <version_command>staramr --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
diff -r 3b22de20bd4b -r 3548a93b39c1 test-data/test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa
--- a/test-data/test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa	Tue Sep 19 18:41:35 2023 +0000
+++ b/test-data/test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa	Wed Dec 18 19:43:50 2024 +0000
@@ -1,4 +1,4 @@
->16S_rrsD isolate: 16S-rc_gyrA-rc_beta-lactam.fsa, contig: 16S_rrsD, contig_start: 1604, contig_end: 61, database_gene_start: 1, database_gene_end: 1544, hsp/length: 1544/1544, pid: 99.94%, plength: 100.00%
+>16S-rrsD_1_CP049983.1 isolate: 16S-rc_gyrA-rc_beta-lactam.fsa, contig: 16S_rrsD, contig_start: 1604, contig_end: 61, database_gene_start: 1, database_gene_end: 1544, hsp/length: 1544/1544, pid: 99.94%, plength: 100.00%
 AATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAG
 TCGAACGGTAACAGGAAGCAGCTTGCTGCTTCGCTGACGAGTGGCGGACGGGTGAGTAAT
 GTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTGGCTAATACCGCATA
@@ -25,7 +25,7 @@
 CCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTA
 GCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAAC
 AAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACCT
->gyrA isolate: 16S-rc_gyrA-rc_beta-lactam.fsa, contig: 16S_rrsD, contig_start: 4317, contig_end: 1681, database_gene_start: 1, database_gene_end: 2637, hsp/length: 2637/2637, pid: 99.96%, plength: 100.00%
+>gyrA_1_MH933946.1 isolate: 16S-rc_gyrA-rc_beta-lactam.fsa, contig: 16S_rrsD, contig_start: 4317, contig_end: 1681, database_gene_start: 1, database_gene_end: 2637, hsp/length: 2637/2637, pid: 99.96%, plength: 100.00%
 ATGAGCGACCTTGCGAGAGAAATTACACCGGTCAACATTGAGGAAGAGCTGAAAAGCTCC
 TATCTGGATTATGCGATGTCGGTCATTGTTGGCCGTGCGCTGCCGGATGTCCGAGATGGC
 CTGAAGCCGGTACACCGTCGCGTACTTTACGCCATGAACGTATTGGGCAATGACTGGAAC