From c67d4478d228bfb64fc04bb75f92f716357ce242 Mon Sep 17 00:00:00 2001
From: Helena <hexylena@galaxians.org>
Date: Thu, 17 Oct 2024 10:42:28 +0200
Subject: [PATCH 1/2] Make abritamr outputs tabular

---
 tools/abritamr/abritamr.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/abritamr/abritamr.xml b/tools/abritamr/abritamr.xml
index 1fc70e044de..31f9edb832e 100644
--- 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>

From 9cf7d406b17bd60f049d08f405db96672de7dae3 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Fri, 18 Oct 2024 10:58:58 +0200
Subject: [PATCH 2/2] Assert column count, ftype

---
 tools/abritamr/abritamr.xml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tools/abritamr/abritamr.xml b/tools/abritamr/abritamr.xml
index 31f9edb832e..fe0edd7492e 100644
--- a/tools/abritamr/abritamr.xml
+++ b/tools/abritamr/abritamr.xml
@@ -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>