--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hamronize_tool.xml	Tue Mar 16 12:38:42 2021 +0000
@@ -0,0 +1,200 @@
+<tool id="hamronize_tool" name="hamronize" version="@VERSION@+galaxy0">
+    <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" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        #set $extra_2_params = str("ariba,srax,csstar,groot").split(",")
+        #set $extra_1_param = $extra_2_params + str("amrfinderplus,rgi,resfinder4,deeparg,kmerresistance,srst2,amrplusplus,resfarms").split(",")
+        
+        hamronize 
+        ${select_tool.tool}
+        --analysis_software_version '${analysis_software_version}'
+        --reference_database_version '${reference_database_version}'
+        --format ${output_format}
+        #if $output_format == "tsv" 
+            --output hamronized.tsv
+        #else
+            --output hamronized.json
+        #end if 
+        
+        #if $select_tool.tool in $extra_1_param
+            --input_file_name $select_tool.input_file_name
+        #end if
+        
+        #if $select_tool.tool in $extra_2_params
+            --reference_database_id $select_tool.reference_database_id
+        #end if
+        
+        $report
+    ]]>    </command>
+
+    <inputs>
+        <param name="report" type="data" format="txt,tabular,tsv" label="Report file"/>
+        <conditional name="select_tool">
+            <param name="tool" type="select" label="Tool">
+                <option value="abricate" selected="true">abricate</option>
+                <option value="amrfinderplus">amrfinderplus</option>
+                <option value="ariba">ariba</option>
+                <option value="rgi">rgi</option>
+                <option value="resfinder">resfinder</option>
+                <option value="resfinder4">resfinder4</option>
+                <option value="srax">srax</option>
+                <option value="deeparg">deeparg</option>
+                <option value="kmerresistance">kmerresistance</option>
+                <option value="srst2">srst2</option>
+                <option value="staramr">staramr</option>
+                <option value="csstar">csstar</option>
+                <option value="amrplusplus">amrplusplus</option>
+                <option value="resfams">resfams</option>
+                <option value="groot">groot</option>
+            </param>
+            <when value="abricate" />
+            <when value="resfinder" />
+            <when value="staramr" />
+            <when value="amrfinderplus">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="ariba">
+                <expand macro="input_file_name"/>
+                <expand macro="reference_database_id"/>
+            </when>
+
+            <when value="rgi">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="resfinder4">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="srax">
+                <expand macro="input_file_name"/>
+                <expand macro="reference_database_id"/>
+            </when>
+
+            <when value="deeparg">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="kmerresistance">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="srst2">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="csstar">
+                <expand macro="input_file_name"/>
+                <expand macro="reference_database_id"/>
+            </when>
+
+            <when value="amrplusplus">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="resfams">
+                <expand macro="input_file_name"/>
+            </when>
+
+            <when value="groot">
+                <expand macro="input_file_name"/>
+                <expand macro="reference_database_id"/>
+            </when>
+        </conditional>
+        <param name="output_format" type="select" label="Output format" multiple="false" display="radio">
+            <option value="tsv" selected="True">tsv</option>
+            <option value="json">json</option>
+        </param>
+        <param name="analysis_software_version" type="text" label="Analysis software version"></param>
+        <param name="reference_database_version" type="text" label="Reference database version"></param>
+    </inputs>
+
+    <outputs>
+        <data format="tsv" 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">
+            <filter>output_format == "json"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- abricate -->
+        <test expect_num_outputs="1">
+            <param name="report" value="abricate/report.tsv" ftype="tsv" />
+            <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" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="report" value="abricate/report.tsv" ftype="tsv" />
+            <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" />
+        </test>
+        <!-- ariba -->
+        <test expect_num_outputs="1">
+            <param name="report" value="ariba/report.tsv" ftype="tsv" />
+            <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" />
+        </test>
+        <!-- rgi -->
+        <test expect_num_outputs="1">
+            <param name="report" value="rgi/rgi.txt" ftype="txt" />
+            <param name="tool" value="rgi" />
+            <param name="output_format" value="tsv" />
+            <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" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    **What it does**
+    Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
+
+    **Inputs**
+    
+    ::
+
+        Tools with hAMRonizable reports:
+        {abricate,amrfinderplus,ariba,rgi,resfinder,resfinder4,srax,deeparg,kmerresistance,srst2,staramr,csstar,amrplusplus,resfams,groot}
+        abricate            hAMRonize abricate's output report i.e., OUTPUT.tsv
+        amrfinderplus       hAMRonize amrfinderplus's output report i.e., OUTPUT.tsv
+        ariba               hAMRonize ariba's output report i.e., OUTDIR/OUTPUT.tsv
+        rgi                 hAMRonize rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
+        resfinder           hAMRonize resfinder's output report i.e., data_resfinder.json
+        resfinder4          hAMRonize resfinder4's tabular output report i.e., ResFinder_results_tab.txt
+        srax                hAMRonize srax's output report i.e., sraX_detected_ARGs.tsv
+        deeparg             hAMRonize deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
+        kmerresistance      hAMRonize kmerresistance's output report i.e., OUTPUT.KmerRes
+        srst2               hAMRonize srst2's output report i.e., OUTPUT_srst2_report.tsv
+        staramr             hAMRonize staramr's output report i.e., resfinder.tsv
+        csstar              hAMRonize csstar's output report i.e., OUTPUT.tsv
+        amrplusplus         hAMRonize amrplusplus's output report i.e., gene.tsv
+        resfams             hAMRonize resfams's output report i.e., resfams.tblout
+        groot               hAMRonize groot's output report i.e., OUTPUT.tsv (from `groot report`)
+    
+
+
+    ::
+    
+    More: https://github.com/pha4ge/hAMRonization/#usage
+
+    ]]>    </help>
+</tool>