--- a/hamronize_summarize.xml	Fri Feb 09 21:27:25 2024 +0000
+++ b/hamronize_summarize.xml	Tue Mar 05 19:47:21 2024 +0000
@@ -1,5 +1,5 @@
-<tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
-    <description> harmorization reports</description>
+<tool id="hamronize_summarize" name="hamronize summarize:" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Concatenate and summarize AMR detection reports</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,45 +7,35 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
-        #for $counter, $report in enumerate($reports):
-            #if $report.is_of_type('tsv', 'tabular'):
-                #set $ext = 'tsv'
-            #elif $report.is_of_type('json'):
-                #set $ext = 'json'
-            #end if
-            ln -s '$report' ./report_${counter}.${ext} &&
-        #end for
+#for $counter, $report in enumerate($reports):
+    #if $report.is_of_type('tsv', 'tabular'):
+        #set $ext = 'tsv'
+    #elif $report.is_of_type('json'):
+        #set $ext = 'json'
+    #end if
+    ln -s '$report' 'report_${counter}.${ext}' &&
+#end for
 
-        hamronize summarize
-        --summary_type $summary_type
-        #if $summary_type == "tsv"
-            --output output.tsv
-        #elif $summary_type == "json"
-            --output output.json
-        #else
-             --output output.html
-        #end if
-        ./report_*
-    ]]>    </command>
-
+hamronize 
+    summarize
+    --summary_type '$summary_type'
+    --output '$output'
+    report_*
+]]></command>
     <inputs>
         <param name="reports" type="data" multiple="true" format="tabular,json" label="Report files"/>
-        <param name="summary_type" type="select" label="Output format" multiple="false">
-            <option value="tsv">tsv</option>
-            <option value="json">json</option>
-            <option value="interactive">interactive</option>
+        <param argument="--summary_type" type="select" label="Output format" multiple="false">
+            <option value="tsv">Tabular</option>
+            <option value="json">JSON</option>
+            <option value="interactive">Interactive HTML</option>
         </param>
     </inputs>
-
     <outputs>
-        <data format="tabular" name="output_tsv" label="${tool.name} on ${on_string}: Table" from_work_dir="output.tsv">
-            <filter>summary_type == "tsv"</filter>
-        </data>
-        <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="output.json">
-            <filter>summary_type == "json"</filter>
-        </data>
-        <data format="html" name="output_html" label="${tool.name} on ${on_string}: Interactive" from_work_dir="output.html">
-            <filter>summary_type == "interactive"</filter>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Concatenated and summarized reports" from_work_dir="output.tsv">
+            <change_format>
+                <when input="summary_type" value="json" format="json"/>
+                <when input="summary_type" value="interactive" format="html"/>
+            </change_format>
         </data>
     </outputs>
     <tests>
@@ -53,30 +43,49 @@
         <test expect_num_outputs="1">
             <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
             <param name="summary_type" value="tsv" />
-            <output name="output_tsv" ftype="tabular" file="summary.tsv" />
+            <output name="output" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="155"/>
+                    <has_n_columns n="37"/>
+                    <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
+                    <has_text text="ariba_report" />
+                    <has_text text="rgi_report" />
+                </assert_contents>
+            </output>
         </test>
         <!-- json output -->
         <test expect_num_outputs="1">
             <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
             <param name="summary_type" value="json" />
-            <output name="output_json" ftype="json">
+            <output name="output" ftype="json">
                 <assert_contents>
                     <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
-                    <has_text text="H_NS.3000676.BA000007.3.1737690_1738104.5476" />
-                    <has_text text="NODE_9_length_203843_cov_42.4911_20" />
+                    <has_text text="ariba_report" />
+                    <has_text text="rgi_report" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- html output -->
+        <test expect_num_outputs="1">
+            <param name="reports" value="hamronized_abricate.tsv,hamronized_abricate.json,hamronized_ariba.tsv,hamronized_ariba.json,hamronized_rgi.tsv,hamronized_rgi.json" />
+            <param name="summary_type" value="interactive" />
+            <output name="output" ftype="html">
+                <assert_contents>
+                    <has_text text="GCF_010120755.1_ASM1012075v1_genomic" />
+                    <has_text text="ariba_report" />
+                    <has_text text="rgi_report" />
                 </assert_contents>
             </output>
         </test>
     </tests>
-    <help>
-        <![CDATA[
-            **What it does**
-            This tool will take a list of report and create single sorted report in the specified format
-            just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
-            **Inputs**
-            A list of hamronize reports
-            
-        ]]>
-    </help>
+    <help><![CDATA[
+**What it does**
+
+This tool will take a list of report and create single sorted report in the specified format
+just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
+
+**Inputs**
+A list of hamronize reports     
+    ]]></help>
     <expand macro="citations"/>
 </tool>