# HG changeset patch
# User iuc
# Date 1707514038 0
# Node ID e13b801516dd6f2b18fdbe5227f253e9dbf6ec53
# Parent  41c7e03b3eab2e157e3bdc2d2471687b958b4b1a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b4943555d76f7e352de3f396c51d3dfb90ed633d

diff -r 41c7e03b3eab -r e13b801516dd hamronize_tool.xml
--- a/hamronize_tool.xml	Fri Aug 05 12:58:22 2022 +0000
+++ b/hamronize_tool.xml	Fri Feb 09 21:27:18 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <expand macro="version_command" />
 
@@ -58,50 +59,39 @@
             <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"/>
@@ -116,10 +106,10 @@
     </inputs>
 
     <outputs>
-        <data format="tabular" 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 ${on_string}: Table" from_work_dir="hamronized.tsv">
             <filter>output_format == "tsv"</filter>
         </data>
-        <data format="json" name="output_json" label="${tool.name} on ${on_string}: Output" from_work_dir="hamronized.json">
+        <data format="json" name="output_json" label="${tool.name} on ${on_string}: JSON" from_work_dir="hamronized.json">
             <filter>output_format == "json"</filter>
         </data>
     </outputs>
@@ -164,36 +154,32 @@
         </test>
     </tests>
     <help><![CDATA[
-    **What it does**
-    Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
+**What it does**
+
+Hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
 
-    **Inputs**
-    
-    ::
+**Inputs**
+
+Depends on the tools with hAMRonizable reports:
 
-        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`)
-    
+* abricate: abricate's output report i.e., OUTPUT.tsv
+* amrfinderplus: amrfinderplus's output report i.e., OUTPUT.tsv
+* ariba: ariba's output report i.e., OUTDIR/OUTPUT.tsv
+* rgi: rgi's output report i.e., OUTPUT.txt or OUTPUT_bwtoutput.gene_mapping_data.txt
+* resfinder: resfinder's output report i.e., data_resfinder.json
+* resfinder4: resfinder4's tabular output report i.e., ResFinder_results_tab.txt
+* srax: srax's output report i.e., sraX_detected_ARGs.tsv
+* deeparg: deeparg's output report i.e., OUTDIR/OUTPUT.mapping.ARG
+* kmerresistance: kmerresistance's output report i.e., OUTPUT.KmerRes
+* srst2: srst2's output report i.e., OUTPUT_srst2_report.tsv
+* staramr: staramr's output report i.e., resfinder.tsv
+* csstar: csstar's output report i.e., OUTPUT.tsv
+* amrplusplus: amrplusplus's output report i.e., gene.tsv
+* resfams: resfams's output report i.e., resfams.tblout
+* groot: groot's output report i.e., OUTPUT.tsv (from `groot report`)
 
+More: https://github.com/pha4ge/hAMRonization/#usage
 
-    ::
-    
-    More: https://github.com/pha4ge/hAMRonization/#usage
-
-    ]]>    </help>
+]]></help>
+    <expand macro="citations"/>
 </tool>
diff -r 41c7e03b3eab -r e13b801516dd macros.xml
--- a/macros.xml	Fri Aug 05 12:58:22 2022 +0000
+++ b/macros.xml	Fri Feb 09 21:27:18 2024 +0000
@@ -1,30 +1,34 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.3</token>
     <token name="@PROFILE@">20.05</token>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">hamronization</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">hamronization</requirement>
         </requirements>
     </xml>
-
     <xml name="input_file_name">
         <param name="input_file_name" type="text" label="Input file name" help="Sample name which was scanned with the tool"></param>
     </xml>
-
     <xml name="reference_database_id">
         <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id of this tool"></param>
     </xml>
-
     <xml name="reference_database_version">
         <param name="reference_database_version" type="text" label="Reference database version"></param>
     </xml>
-
     <xml name="analysis_software_version">
         <param name="analysis_software_version" type="text" label="Analysis software version"></param>
     </xml>
-
     <xml name="version_command">
         <version_command>hamronize --version</version_command>
     </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.5281/zenodo.10015946</citation>
+        </citations>
+    </xml>
 </macros>