--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hamronize_summarize.xml	Tue Mar 16 12:39:05 2021 +0000
@@ -0,0 +1,82 @@
+<tool id="hamronize_summarize" name="summarize" version="@VERSION@+galaxy0">
+    <description> harmorization reports</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <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
+
+        hamronize summarize
+        --summary_type $summary_type
+        #if $summary_type == "tsv" 
+            --output output.tsv
+        #elif $summary_type == "json"
+            --output output.json
+        #else 
+             --output output.html
+        #end if
+        *.tsv
+        *.json
+    ]]>    </command>
+
+    <inputs>
+        <param name="reports" type="data" multiple="true" format="tsv,json" label="Report files"/>
+        <param name="summary_type" type="select" label="Output format" multiple="false">
+            <option value="tsv">tsv</option>
+            <option value="json">json</option>
+            <option value="interactive">interactive</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="tsv" name="output_tsv" label="${tool.name} on ${on_string}: Output" from_work_dir="output.tsv">
+            <filter>summary_type == "tsv"</filter>
+        </data>
+        <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="output.json">
+            <filter>summary_type == "json"</filter>
+        </data>
+        <data format="html" name="output_html" label="${tool.name} on ${on_string}: Output" from_work_dir="output.html">
+            <filter>summary_type == "interactive"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- tsv 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="tsv" />
+            <output name="output_tsv" ftype="tsv" file="summary.tsv" />
+        </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">
+                <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" />
+                </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>
+</tool>