Merge branch 'master' into sistr

phac-nml · Dec 19, 2024 · ab34281 · ab34281
2 parents 8e069fd + f574c20
commit ab34281
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Showing 4 changed files with 12 additions and 10 deletions.
diff --git a/tools/ectyper/.shed.yml b/tools/ectyper/.shed.yml
@@ -3,5 +3,5 @@ description: EC-Typer - in silico serotyping of Escherichia coli species
 name: ectyper
 owner: nml
 long_description: EC-Typer is a standalone serotyping module for Escherichia coli typing. It supports fasta and fastq file formats. Designed by Chad Liang et al.
-remote_repository_url: https://github.com/phac-nml/ecoli_serotyping
+remote_repository_url: https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper
 homepage_url: https://github.com/phac-nml/ecoli_serotyping
diff --git a/tools/ectyper/ectyper.xml b/tools/ectyper/ectyper.xml
@@ -1,5 +1,8 @@
 <tool id="ectyper" name="ectyper" version="1.0.0">
   <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
+  <xrefs>
+    <xref type="bio.tools">ectyper</xref>
+  </xrefs>
   <requirements>
      <requirement type="package" version="1.0.0">ectyper</requirement>
   </requirements>
@@ -76,7 +79,7 @@
     </data>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="1">
       <param name="input" value="Escherichia2.fastq"/>
       <assert_stderr>
             <has_text text="O22"/> 

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