Merge pull request #6462 from galaxyproject/hexylena-patch-1

Make abritamr outputs tabular
galaxyproject · Oct 19, 2024 · 1550e33 · 1550e33
2 parents d3549bc + 9cf7d40
commit 1550e33
Showing 1 changed file with 9 additions and 7 deletions.
diff --git a/tools/abritamr/abritamr.xml b/tools/abritamr/abritamr.xml
@@ -2,7 +2,7 @@
     <description>AMR gene detection with AMRFinderPlus</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0.19</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PROFILE@">22.05</token>
     </macros>
     <xrefs>
@@ -51,10 +51,10 @@ ${i.element_identifier}	${i}
         <param name="log_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate log file."/>
     </inputs>
     <outputs>
-        <data name="abriTAMR_output" format="txt" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
-        <data name="matches_summary" format="txt" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
-        <data name="partials_summary" format="txt" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
-        <data name="virulence_summary" format="txt" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
+        <data name="abriTAMR_output" format="tabular" label="${tool.name} on ${on_string}: abriTAMR.txt" from_work_dir="abritamr.txt" />
+        <data name="matches_summary" format="tabular" label="${tool.name} on ${on_string}: matches summary" from_work_dir="summary_matches.txt"/>
+        <data name="partials_summary" format="tabular" label="${tool.name} on ${on_string}: partials summary" from_work_dir="summary_partials.txt"/>
+        <data name="virulence_summary" format="tabular" label="${tool.name} on ${on_string}: virulence summary" from_work_dir="summary_virulence.txt"/>
         <data name="log" format="txt" label="${tool.name} on ${on_string}: log file" from_work_dir="abritamr.log">
             <filter>log_file</filter>
         </data>
@@ -64,10 +64,11 @@ ${i.element_identifier}	${i}
         <test expect_num_outputs="5">
             <param name="contig" value="CP009102.1.fasta" />
             <param name="log_file" value="true" />
-            <output name="virulence_summary" ftype="txt">
+            <output name="virulence_summary" ftype="tabular">
                 <assert_contents>
                     <has_n_lines n="2"/>
                     <has_text text="sinH"/>
+                    <has_n_columns n="2"/>
                 </assert_contents>
             </output>
         </test>
@@ -77,10 +78,11 @@ ${i.element_identifier}	${i}
             <param name="species" value="Salmonella" />
             <param name="identity" value="0.9" />
             <param name="log_file" value="false" />
-            <output name="virulence_summary" ftype="txt">
+            <output name="virulence_summary" ftype="tabular">
                 <assert_contents>
                     <has_n_lines n="3"/>
                     <has_text text="NC_003198.1_1kb.fasta"/>
+                    <has_n_columns n="1"/>
                 </assert_contents>
             </output>
         </test>