Mercurial > repos > iuc > abritamr

changeset 5:468fd92deaaa draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr commit 1550e33e5b13d9e8761c362e47fc473721a13d5a
author iuc
date Sat, 19 Oct 2024 20:56:13 +0000
parents e909d3bc4687
children
files abritamr.xml
diffstat 1 files changed, 9 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/abritamr.xml	Mon Sep 09 09:01:11 2024 +0000
+++ b/abritamr.xml	Sat Oct 19 20:56:13 2024 +0000
@@ -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 @@
         <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 @@
         <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 @@
             <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>