--- a/hamronize_tool.xml	Tue Mar 16 12:38:42 2021 +0000
+++ b/hamronize_tool.xml	Sat Oct 23 21:38:09 2021 +0000
@@ -1,9 +1,8 @@
-<tool id="hamronize_tool" name="hamronize" version="@VERSION@+galaxy0">
+<tool id="hamronize_tool" name="hamronize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description> parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-
     <expand macro="requirements" />
     <expand macro="version_command" />
 
@@ -34,7 +33,7 @@
     ]]>    </command>
 
     <inputs>
-        <param name="report" type="data" format="txt,tabular,tsv" label="Report file"/>
+        <param name="report" type="data" format="txt,tabular" label="Report file"/>
         <conditional name="select_tool">
             <param name="tool" type="select" label="Tool">
                 <option value="abricate" selected="true">abricate</option>
@@ -117,7 +116,7 @@
     </inputs>
 
     <outputs>
-        <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv">
+        <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.tsv">
             <filter>output_format == "tsv"</filter>
         </data>
         <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json">
@@ -127,31 +126,31 @@
     <tests>
         <!-- abricate -->
         <test expect_num_outputs="1">
-            <param name="report" value="abricate/report.tsv" ftype="tsv" />
+            <param name="report" value="abricate/report.tsv" ftype="tabular" />
             <param name="tool" value="abricate" />
             <param name="output_format" value="tsv" />
             <param name="reference_database_version" value="db_v_1" />
             <param name="analysis_software_version" value="tool_v_1" />
-            <output name="output_tsv" ftype="tsv" file="hamronized_abricate.tsv" />
+            <output name="output_tsv" file="hamronized_abricate.tsv" ftype="tabular" />
         </test>
         <test expect_num_outputs="1">
-            <param name="report" value="abricate/report.tsv" ftype="tsv" />
+            <param name="report" value="abricate/report.tsv" ftype="tabular" />
             <param name="tool" value="abricate" />
             <param name="output_format" value="json" />
             <param name="reference_database_version" value="db_v_1" />
             <param name="analysis_software_version" value="tool_v_1" />
-            <output name="output_json" ftype="json" file="hamronized_abricate.json" />
+            <output name="output_json" file="hamronized_abricate.json" ftype="json" />
         </test>
         <!-- ariba -->
         <test expect_num_outputs="1">
-            <param name="report" value="ariba/report.tsv" ftype="tsv" />
+            <param name="report" value="ariba/report.tsv" ftype="tabular" />
             <param name="tool" value="ariba" />
             <param name="output_format" value="tsv" />
             <param name="reference_database_version" value="db_v_1" />
             <param name="analysis_software_version" value="ariba_v1" />
             <param name="input_file_name" value="ariba_report" />
             <param name="reference_database_id" value="dbname" />
-            <output name="output_tsv" ftype="tsv" file="hamronized_ariba.tsv" />
+            <output name="output_tsv" file="hamronized_ariba.tsv" ftype="tabular" />
         </test>
         <!-- rgi -->
         <test expect_num_outputs="1">
@@ -161,7 +160,7 @@
             <param name="reference_database_version" value="card_v1" />
             <param name="analysis_software_version" value="rgi_v1" />
             <param name="input_file_name" value="rgi_report" />
-            <output name="output_tsv" ftype="tsv" file="hamronized_rgi.tsv" />
+            <output name="output_tsv" file="hamronized_rgi.tsv" ftype="tabular"/>
         </test>
     </tests>
     <help><![CDATA[