Merge pull request #270 from phac-nml/update/staramr

Update StarAMR to 0.11.0
phac-nml · Dec 18, 2024 · b534dcd · b534dcd
2 parents 97945a3 + 56a73b7
commit b534dcd
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Showing 2 changed files with 7 additions and 8 deletions.
diff --git a/tools/staramr/staramr_search.xml b/tools/staramr/staramr_search.xml
@@ -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 --git a/tools/staramr/test-data/test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa b/tools/staramr/test-data/test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa
@@ -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 @@ CGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTT
 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